Query 019224
Match_columns 344
No_of_seqs 33 out of 35
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 07:43:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019224.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019224hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10077 DUF2314: Uncharacteri 16.2 1.7E+02 0.0038 25.5 3.4 25 281-306 47-71 (133)
2 cd02566 PseudoU_synth_RluE Pse 11.8 2.2E+02 0.0048 25.1 2.9 25 125-149 139-165 (168)
3 KOG4469 Uncharacterized conser 11.5 1.8E+02 0.0039 29.0 2.4 36 286-321 322-364 (391)
4 PF14784 ECIST_Cterm: C-termin 10.8 1.5E+02 0.0033 26.2 1.5 16 47-62 15-30 (126)
5 PF13257 DUF4048: Domain of un 10.4 90 0.0019 30.7 -0.1 21 114-134 91-111 (253)
6 PF00313 CSD: 'Cold-shock' DNA 8.5 4.5E+02 0.0099 19.3 3.2 28 280-309 39-66 (66)
7 PF04969 CS: CS domain; Inter 8.4 6.9E+02 0.015 18.0 4.1 37 57-93 4-43 (79)
8 cd06479 ACD_HspB7_like Alpha c 8.4 3.3E+02 0.0072 21.8 2.5 22 66-87 53-74 (81)
9 smart00874 B5 tRNA synthetase 8.3 76 0.0016 23.8 -1.2 44 227-281 10-53 (71)
10 PF09157 TruB-C_2: Pseudouridi 8.0 3.1E+02 0.0067 19.9 2.0 22 285-306 30-57 (58)
No 1
>PF10077 DUF2314: Uncharacterized protein conserved in bacteria (DUF2314); InterPro: IPR018756 This domain of unkown function is found in various bacterial hypothetical proteins, as well as putative ankyrin repeat proteins.
Probab=16.18 E-value=1.7e+02 Score=25.51 Aligned_cols=25 Identities=20% Similarity=0.262 Sum_probs=20.2
Q ss_pred cccceEEEeEEEEEEecCCceeeeee
Q 019224 281 TKPETVKLHFEVLAKVDGEKVIPERV 306 (344)
Q Consensus 281 TkP~~~R~~fEVlAkVeg~kl~p~~V 306 (344)
.-+..|||||+++.. +|++.+-..+
T Consensus 47 ~~~~~EhmWv~~~~~-~g~~~~G~L~ 71 (133)
T PF10077_consen 47 DEPNVEHMWVEVVDF-DGDTFSGVLD 71 (133)
T ss_pred CCCceeEEEEEEEEe-cCCEEEEEEe
Confidence 456789999999998 9998875544
No 2
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved.
Probab=11.83 E-value=2.2e+02 Score=25.07 Aligned_cols=25 Identities=40% Similarity=0.671 Sum_probs=21.5
Q ss_pred HHHHHhhhhcCCCeeeE-EE-ecccee
Q 019224 125 EQLRHASRAQGAPLLSL-RI-VGPTSL 149 (344)
Q Consensus 125 ~~Lr~as~s~~~PLLsl-rI-VGp~sL 149 (344)
+|||.-..+-+.|++.| || +|+..|
T Consensus 139 HQIR~~la~lG~pV~~L~R~~~g~~~l 165 (168)
T cd02566 139 RQVRRMTAAVGFPTLRLIRVSIGDIGL 165 (168)
T ss_pred HHHHHHHHHcCCeEeEEEEEEECCEEc
Confidence 59999999999999999 77 787665
No 3
>KOG4469 consensus Uncharacterized conserved protein [Function unknown]
Probab=11.49 E-value=1.8e+02 Score=28.95 Aligned_cols=36 Identities=28% Similarity=0.273 Sum_probs=23.3
Q ss_pred EEEeEEEEEEecCCceeeeeeeeecc-------cccccccccc
Q 019224 286 VKLHFEVLAKVDGEKVIPERVVQVNP-------FDVEDTVAPN 321 (344)
Q Consensus 286 ~R~~fEVlAkVeg~kl~p~~V~qV~P-------~~~~dt~s~s 321 (344)
-|+|||....-|-+-+.=--|.|-+| ...+||.||.
T Consensus 322 wrlhfefvtsrepglvllppveqpepttwtgpeqvpvdtfswd 364 (391)
T KOG4469|consen 322 WRLHFEFVTSREPGLVLLPPVEQPEPTTWTGPEQVPVDTFSWD 364 (391)
T ss_pred eEEEEEEEecCCCCeEecCCcCCCCCccccCCccccccccccc
Confidence 37899988888855443333444443 3468899996
No 4
>PF14784 ECIST_Cterm: C-terminal domain of the ECSIT protein
Probab=10.76 E-value=1.5e+02 Score=26.15 Aligned_cols=16 Identities=31% Similarity=0.989 Sum_probs=13.4
Q ss_pred cCceecCceEEEEecC
Q 019224 47 APFQLAGPMELWIQDA 62 (344)
Q Consensus 47 ~~f~L~GP~ELwi~~~ 62 (344)
.|+-++|||-+|+.+.
T Consensus 15 ~PvfVEGPf~vwLrd~ 30 (126)
T PF14784_consen 15 EPVFVEGPFSVWLRDK 30 (126)
T ss_pred CcEEEECCcEEEEcCc
Confidence 4778999999999874
No 5
>PF13257 DUF4048: Domain of unknown function (DUF4048)
Probab=10.36 E-value=90 Score=30.65 Aligned_cols=21 Identities=33% Similarity=0.616 Sum_probs=18.0
Q ss_pred CCCccchHHHHHHHHHhhhhc
Q 019224 114 NGFASGLLTLAEQLRHASRAQ 134 (344)
Q Consensus 114 ~~~~sgl~~la~~Lr~as~s~ 134 (344)
.+|..|||+|.|-||+|-=..
T Consensus 91 eDfK~GLWTFvEDIRQATVGD 111 (253)
T PF13257_consen 91 EDFKEGLWTFVEDIRQATVGD 111 (253)
T ss_pred HHHHHHHHHHHHHHHHhhccc
Confidence 568999999999999998543
No 6
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=8.53 E-value=4.5e+02 Score=19.33 Aligned_cols=28 Identities=21% Similarity=0.232 Sum_probs=19.7
Q ss_pred ccccceEEEeEEEEEEecCCceeeeeeeee
Q 019224 280 RTKPETVKLHFEVLAKVDGEKVIPERVVQV 309 (344)
Q Consensus 280 rTkP~~~R~~fEVlAkVeg~kl~p~~V~qV 309 (344)
+.-=.=+++.|++-. ..+++.+..|+++
T Consensus 39 ~~l~~G~~V~F~~~~--~~~g~~A~~V~~~ 66 (66)
T PF00313_consen 39 RSLKEGDRVEFEVEE--GKKGPQAVNVRKI 66 (66)
T ss_dssp TS--TTSEEEEEEEE--CTTSEEEEEEEE-
T ss_pred ccCCCCCEEEEEEEE--CCCCCEEEEEECc
Confidence 333345789999988 8888888888763
No 7
>PF04969 CS: CS domain; InterPro: IPR017447 The function of the CS domain is unknown. The CS domain is sometimes found C-terminal to the CHORD domain (IPR007051 from INTERPRO) in metazoan proteins, but occurs separately from the CHORD domain in plants. This association is thought to be indicative of an functional interaction between CS and CHORD domains [].; PDB: 1WGV_A 2KMW_A 2O30_B 1WH0_A 1EJF_A 2RH0_B 1RL1_A 2CR0_A 1WFI_A 2XCM_D ....
Probab=8.44 E-value=6.9e+02 Score=17.98 Aligned_cols=37 Identities=19% Similarity=0.354 Sum_probs=23.6
Q ss_pred EEEecCCCeeeeccc-cCC--ccceeEEEecCCcEEEEcc
Q 019224 57 LWIQDAKDMRISLPH-DVD--AGVLKKVVLADGAVVTVNG 93 (344)
Q Consensus 57 Lwi~~~~~~~L~LP~-~vd--ag~LKrVlla~Ga~V~V~G 93 (344)
-|=|..+.+.+.++. +.. ...++=-+=.+...|++++
T Consensus 4 ~W~Qt~~~V~v~i~~~~~~~~~~dv~v~~~~~~l~v~~~~ 43 (79)
T PF04969_consen 4 DWYQTDDEVTVTIPVKPVDISKEDVKVDFTDTSLSVSIKS 43 (79)
T ss_dssp EEEEESSEEEEEEE-TTTTSSGGGEEEEEETTEEEEEEEE
T ss_pred EEEECCCEEEEEEEEcCCCCChHHeEEEEEeeEEEEEEEc
Confidence 378888888777777 443 4556555556666666663
No 8
>cd06479 ACD_HspB7_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB7, also known as cardiovascular small heat shock protein (cvHsp), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB7 is a 25-kDa protein, preferentially expressed in heart and skeletal muscle. It binds the cytoskeleton protein alpha-filamin (also known as actin-binding protein 280). The expression of HspB7 is increased during rat muscle aging. Its expression is also modulated in obesity implicating this protein in this and related metabolic disorders. As the human gene encoding HspB7 is mapped to chromosome 1p36.23-p34.3 it is a positional candidate for several dystrophies and myopathies.
Probab=8.41 E-value=3.3e+02 Score=21.77 Aligned_cols=22 Identities=32% Similarity=0.533 Sum_probs=19.2
Q ss_pred eeeccccCCccceeEEEecCCc
Q 019224 66 RISLPHDVDAGVLKKVVLADGA 87 (344)
Q Consensus 66 ~L~LP~~vdag~LKrVlla~Ga 87 (344)
++.||.++|...++--+-++|+
T Consensus 53 ~~~LP~~vd~e~v~A~l~~~Gv 74 (81)
T cd06479 53 KCQLPEDVDPTSVSSSLGEDGT 74 (81)
T ss_pred EEECCCCcCHHHeEEEecCCCE
Confidence 7899999999988888778886
No 9
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=8.30 E-value=76 Score=23.77 Aligned_cols=44 Identities=25% Similarity=0.480 Sum_probs=24.1
Q ss_pred HHHHhhCCccccccceeeEEeeeeeeeEEEEeeeEeeeccCCCCCCCCCCccCcc
Q 019224 227 LLSSVLGPKAKQKGSFKLLKADVSAQTFLKIGFGVEKKLKEGDGFDLEGFPEWRT 281 (344)
Q Consensus 227 lL~s~Lg~k~~~~gsf~llkA~vsA~t~Vk~~felEk~i~~~~~~~~e~~PeWrT 281 (344)
-+++++|.....+...++|+ +++|++|. -.+++.... ..|.||.
T Consensus 10 ~i~~llG~~i~~~ei~~~L~---------~lg~~~~~-~~~~~~~~v-~~P~~R~ 53 (71)
T smart00874 10 RINRLLGLDLSAEEIEEILK---------RLGFEVEV-SGDDDTLEV-TVPSYRF 53 (71)
T ss_pred HHHHHHCCCCCHHHHHHHHH---------HCCCeEEe-cCCCCeEEE-ECCCCcc
Confidence 34556776655544444444 66777765 121233332 6788884
No 10
>PF09157 TruB-C_2: Pseudouridine synthase II TruB, C-terminal; InterPro: IPR015240 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. The C-terminal domain adopts a secondary structure consisting of a four-stranded beta sheet and one alpha helix, similar to that found in PUA domains. It is predominantly involved in RNA-binding, being mostly found in tRNA pseudouridine synthase B (TruB) []. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1ZL3_A 1K8W_A 1R3F_A.
Probab=8.04 E-value=3.1e+02 Score=19.94 Aligned_cols=22 Identities=23% Similarity=0.525 Sum_probs=14.1
Q ss_pred eEEEe-----EEEEEEec-CCceeeeee
Q 019224 285 TVKLH-----FEVLAKVD-GEKVIPERV 306 (344)
Q Consensus 285 ~~R~~-----fEVlAkVe-g~kl~p~~V 306 (344)
..|++ |==|++++ +++++|.++
T Consensus 30 ~vrvy~~~~~FlGig~~~~~g~L~P~Rl 57 (58)
T PF09157_consen 30 LVRVYDEDGRFLGIGEIDDDGRLKPKRL 57 (58)
T ss_dssp EEEEETTTTEEEEEEEE-TTS-EEEEEE
T ss_pred eEEEECCCCEEEEEEEEccCCEEEeeEc
Confidence 45555 55677888 888888876
Done!