Query psy17970
Match_columns 174
No_of_seqs 4 out of 6
Neff 1.8
Searched_HMMs 46136
Date Fri Aug 16 19:02:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17970.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17970hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3391 Uncharacterized conser 6.1 1.7E+03 0.036 19.1 11.1 110 53-162 122-244 (381)
2 PF07179 SseB: SseB protein N- 4.3 5.1E+02 0.011 17.5 1.3 13 23-35 105-117 (124)
3 PF06093 Spt4: Spt4/RpoE2 zinc 3.7 3.3E+02 0.0072 19.7 -0.1 11 42-52 49-59 (77)
4 cd00769 PheRS_beta_core Phenyl 3.1 3.8E+02 0.0082 20.7 -0.3 18 30-47 42-59 (198)
5 PF03725 RNase_PH_C: 3' exorib 3.1 2.4E+02 0.0053 18.1 -1.2 14 3-16 16-29 (68)
6 PRK06393 rpoE DNA-directed RNA 3.1 4.3E+02 0.0092 19.0 -0.0 9 43-51 38-46 (64)
7 cd07973 Spt4 Transcription elo 2.7 4.8E+02 0.01 19.7 -0.1 12 41-52 51-62 (98)
8 PRK08351 DNA-directed RNA poly 2.7 5.3E+02 0.011 18.3 0.1 9 33-41 36-44 (61)
9 KOG1614|consensus 2.4 5.7E+02 0.012 23.3 -0.1 14 3-16 206-219 (291)
10 KOG1364|consensus 2.1 9.4E+02 0.02 22.4 0.9 13 98-110 155-167 (356)
No 1
>COG3391 Uncharacterized conserved protein [Function unknown]
Probab=6.08 E-value=1.7e+03 Score=19.12 Aligned_cols=110 Identities=17% Similarity=0.235 Sum_probs=62.3
Q ss_pred eecCCCCceeeecc--cccceeeecccccceeeecCC--CCceeeeCCCCCceeeecccccceeeecccccceE------
Q psy17970 53 VMDPTLPEMTLMDP--TLSEMTVMDPTLSEMTVMDPT--LPEMTVMDPTLPEMAVMDPTLSEMTVMDPTLSEMT------ 122 (174)
Q Consensus 53 V~~P~~~~~~~l~P--ttse~tv~~Pttse~Tv~~Pt--t~~~~VlnP~~~~~~VlnP~~S~~~VlnP~~S~v~------ 122 (174)
..+|....+-+.|. -...+.+||+.+...+.-.|+ .|..-..+|....+-|.|=-.+.+.++|+-.-++.
T Consensus 122 ~~~~~~~~vYV~n~~~~~~~vsvid~~t~~~~~~~~vG~~P~~~a~~p~g~~vyv~~~~~~~v~vi~~~~~~v~~~~~~~ 201 (381)
T COG3391 122 AVDPDGKYVYVANAGNGNNTVSVIDAATNKVTATIPVGNTPTGVAVDPDGNKVYVTNSDDNTVSVIDTSGNSVVRGSVGS 201 (381)
T ss_pred EECCCCCEEEEEecccCCceEEEEeCCCCeEEEEEecCCCcceEEECCCCCeEEEEecCCCeEEEEeCCCcceecccccc
Confidence 44555556666666 346666777766666655666 46666777777777777755666677775444444
Q ss_pred -eecCCCCceEeecccccceEeeccccc--ceEeeccccccee
Q psy17970 123 -IMDPTLPEMTVMDPTLSEMTVMDPTLS--EMTVMDPTLSEMT 162 (174)
Q Consensus 123 -vlnP~~~~v~VlnP~~S~v~VlnP~~S--~v~VlnP~~S~~~ 162 (174)
+-.-..|.....+|...++-|.+=-.. .+-+.|..+..+.
T Consensus 202 ~~~~~~~P~~i~v~~~g~~~yV~~~~~~~~~v~~id~~~~~v~ 244 (381)
T COG3391 202 LVGVGTGPAGIAVDPDGNRVYVANDGSGSNNVLKIDTATGNVT 244 (381)
T ss_pred ccccCCCCceEEECCCCCEEEEEeccCCCceEEEEeCCCceEE
Confidence 222334455556666665555544432 4444444444443
No 2
>PF07179 SseB: SseB protein N-terminal domain; InterPro: IPR009839 This family consists of several SseB proteins, which appear to be found exclusively in Enterobacteria. SseB is known to enhance serine-sensitivity in Escherichia coli [] and is part of the Salmonella pathogenicity island 2 (SPI-2) translocon [].
Probab=4.31 E-value=5.1e+02 Score=17.53 Aligned_cols=13 Identities=23% Similarity=0.529 Sum_probs=6.7
Q ss_pred eecCCCCceeeeC
Q psy17970 23 VMDPTLPEMTIMD 35 (174)
Q Consensus 23 V~~P~~~~~~i~~ 35 (174)
|+||+++.-.+++
T Consensus 105 viNP~~~~~~~l~ 117 (124)
T PF07179_consen 105 VINPGTPSGFVLP 117 (124)
T ss_pred EEECCCCceEEEC
Confidence 5666666533333
No 3
>PF06093 Spt4: Spt4/RpoE2 zinc finger; InterPro: IPR022800 This entry consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 []. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles []. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in []. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery. ; PDB: 2EXU_A 3H7H_A 3LPE_F 3P8B_A 1RYQ_A 3QQC_E.
Probab=3.69 E-value=3.3e+02 Score=19.66 Aligned_cols=11 Identities=55% Similarity=0.661 Sum_probs=4.1
Q ss_pred eeeccccceee
Q psy17970 42 AVMDPTLSEMA 52 (174)
Q Consensus 42 ~V~~P~~S~~~ 52 (174)
+++||.-|++|
T Consensus 49 ~i~~P~~SwvA 59 (77)
T PF06093_consen 49 AIMDPEKSWVA 59 (77)
T ss_dssp EES-TTT-HHH
T ss_pred EECCCchhHHH
Confidence 44444444443
No 4
>cd00769 PheRS_beta_core Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer. While the alpha chain contains a catalytic core domain, the beta chain has a non-catalytic core domain.
Probab=3.12 E-value=3.8e+02 Score=20.72 Aligned_cols=18 Identities=17% Similarity=0.399 Sum_probs=10.4
Q ss_pred ceeeeCccccceeeeccc
Q psy17970 30 EMTIMDPTLSEMAVMDPT 47 (174)
Q Consensus 30 ~~~i~~P~~S~~~V~~P~ 47 (174)
.++|+||..++..+|=+.
T Consensus 42 ~i~l~NPis~e~~~lR~s 59 (198)
T cd00769 42 AVELSNPLSEEYSVLRTS 59 (198)
T ss_pred eEEEcCCCchhHHHHHHH
Confidence 366666666666655443
No 5
>PF03725 RNase_PH_C: 3' exoribonuclease family, domain 2 This Prosite family only includes Ribonuclease PH; InterPro: IPR015847 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 2, which has a core 3-layer alpha/beta/alpha structure. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 2NN6_E 2WNR_A 3U1K_B 2BA0_H 2BA1_H 3M85_G 3M7N_H 3H1C_K ....
Probab=3.07 E-value=2.4e+02 Score=18.08 Aligned_cols=14 Identities=43% Similarity=0.643 Sum_probs=6.2
Q ss_pred ccCcccccceeccc
Q psy17970 3 VMDPTLSEMAVMDP 16 (174)
Q Consensus 3 V~~P~~S~~~V~~P 16 (174)
++||+..||+.-+.
T Consensus 16 v~Dpt~~Ee~~~~~ 29 (68)
T PF03725_consen 16 VVDPTAEEESLSDS 29 (68)
T ss_dssp EES--HHHHHHSSE
T ss_pred EECCCHHHHhhcCC
Confidence 45555555554443
No 6
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=3.05 E-value=4.3e+02 Score=19.02 Aligned_cols=9 Identities=22% Similarity=0.482 Sum_probs=3.5
Q ss_pred eecccccee
Q psy17970 43 VMDPTLSEM 51 (174)
Q Consensus 43 V~~P~~S~~ 51 (174)
++||.-|++
T Consensus 38 i~dPe~S~v 46 (64)
T PRK06393 38 ITEPEGSAI 46 (64)
T ss_pred EECCchhHH
Confidence 334443333
No 7
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=2.74 E-value=4.8e+02 Score=19.73 Aligned_cols=12 Identities=50% Similarity=0.639 Sum_probs=5.9
Q ss_pred eeeeccccceee
Q psy17970 41 MAVMDPTLSEMA 52 (174)
Q Consensus 41 ~~V~~P~~S~~~ 52 (174)
+++|||.-|++|
T Consensus 51 i~i~dP~~SwVA 62 (98)
T cd07973 51 IALMDPEKSWVA 62 (98)
T ss_pred EEEECCchhHHH
Confidence 344555555544
No 8
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=2.68 E-value=5.3e+02 Score=18.27 Aligned_cols=9 Identities=33% Similarity=0.423 Sum_probs=3.6
Q ss_pred eeCccccce
Q psy17970 33 IMDPTLSEM 41 (174)
Q Consensus 33 i~~P~~S~~ 41 (174)
|+||.-|++
T Consensus 36 I~dPe~S~I 44 (61)
T PRK08351 36 IIDVENSRI 44 (61)
T ss_pred EeCCcHhHH
Confidence 334444433
No 9
>KOG1614|consensus
Probab=2.37 E-value=5.7e+02 Score=23.33 Aligned_cols=14 Identities=64% Similarity=0.781 Sum_probs=10.3
Q ss_pred ccCcccccceeccc
Q psy17970 3 VMDPTLSEMAVMDP 16 (174)
Q Consensus 3 V~~P~~S~~~V~~P 16 (174)
|+||+.-|++++|=
T Consensus 206 viDpt~~Ee~~~dG 219 (291)
T KOG1614|consen 206 VIDPTEKEEAVMDG 219 (291)
T ss_pred EeCCcHHHHhccCc
Confidence 67777777777774
No 10
>KOG1364|consensus
Probab=2.12 E-value=9.4e+02 Score=22.44 Aligned_cols=13 Identities=46% Similarity=0.945 Sum_probs=0.0
Q ss_pred CCceeeecccccc
Q psy17970 98 LPEMAVMDPTLSE 110 (174)
Q Consensus 98 ~~~~~VlnP~~S~ 110 (174)
+|+|+++||.+++
T Consensus 155 ~P~i~iiDp~Tge 167 (356)
T KOG1364|consen 155 LPHIAIIDPITGE 167 (356)
T ss_pred CceEEEECCchhh
Done!