Query 027342
Match_columns 224
No_of_seqs 17 out of 19
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 08:31:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027342.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027342hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08208 RNA_polI_A34: DNA-dir 98.3 9.9E-07 2.1E-11 73.7 5.2 84 29-114 2-95 (198)
2 TIGR02276 beta_rpt_yvtn 40-res 36.2 1E+02 0.0022 18.6 5.4 39 49-88 3-41 (42)
3 PF15174 PRNT: Prion-related p 32.7 10 0.00023 27.4 -0.7 11 33-43 29-39 (51)
4 PF11197 DUF2835: Protein of u 30.6 40 0.00087 25.3 2.0 29 37-66 33-67 (68)
5 TIGR03352 VI_chp_3 type VI sec 30.4 83 0.0018 26.0 4.0 58 22-89 76-139 (146)
6 COG3338 Cah Carbonic anhydrase 27.9 47 0.001 30.8 2.4 36 47-85 85-120 (250)
7 PRK12694 flgG flagellar basal 26.3 1.7E+02 0.0036 26.0 5.5 22 104-125 172-193 (260)
8 cd06479 ACD_HspB7_like Alpha c 26.2 1.6E+02 0.0036 22.0 4.7 31 27-60 2-32 (81)
9 PTZ00363 rab-GDP dissociation 25.1 2E+02 0.0043 27.6 6.1 21 96-116 294-314 (443)
10 PRK12691 flgG flagellar basal 24.5 1.6E+02 0.0035 26.0 5.1 22 104-125 172-193 (262)
11 PRK12819 flgG flagellar basal 24.5 90 0.002 27.7 3.5 26 97-124 166-191 (257)
12 PF11720 Inhibitor_I78: Peptid 23.7 1.8E+02 0.0039 20.6 4.3 20 45-64 37-56 (60)
13 PF04435 SPK: Domain of unknow 23.2 19 0.00041 26.9 -0.9 38 33-71 67-106 (109)
14 PRK12693 flgG flagellar basal 23.0 1.8E+02 0.0039 25.6 5.0 22 104-125 172-193 (261)
15 cd01726 LSm6 The eukaryotic Sm 22.9 46 0.00099 23.7 1.1 37 40-80 1-41 (67)
No 1
>PF08208 RNA_polI_A34: DNA-directed RNA polymerase I subunit RPA34.5; InterPro: IPR013240 This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription [].; PDB: 3NFG_N.
Probab=98.29 E-value=9.9e-07 Score=73.68 Aligned_cols=84 Identities=20% Similarity=0.349 Sum_probs=50.2
Q ss_pred CCCceeEEEecCCCCC-CCCCCceeEEeecCCcceeeeecCCCCeeeeeecc---CCCCCeeEEeeCCCCCc---cccee
Q 027342 29 IDSTELWLIQWPYKQM-PDFDGKELSLELRGNGRLGSFEDSSGKAYDIVSND---FQEPDEMVFLNYPSEPK---IVGKI 101 (224)
Q Consensus 29 tDStELWLIQ~P~~~~-~Df~G~~lslkl~~DG~Lg~Fe~SsGK~YdlVS~~---aq~pdatvfvpS~~e~~---ivgKI 101 (224)
.++.|||||++|.+.- .+|+|..|.|.--.+|. .-|+ -.|..|.|.+.. ......+||||+..... ..-.|
T Consensus 2 ~~~kelWlI~~P~~~~~~~l~~l~i~l~~~~~~~-~~~~-~~~~~Y~i~~~~~~~~~~~~~~lL~p~~~~~~~~~~~~~~ 79 (198)
T PF08208_consen 2 LDGKELWLIKAPASFPISSLKGLPIPLSKSQTGK-PILK-HKGKDYQISEDSINQEESSSISLLLPSKKGGGYLVASKPF 79 (198)
T ss_dssp STTEEEEEEEEETTS-GGG-SEE---S---SBSE-EEEE-ETTEEEEEEEGGGSGS--TTEEEEEE-SSSTTEEESB---
T ss_pred CCCCEEEEEeCCCCCCHHHhCCceeeeeeccCCc-ccee-eCCceEEEEecccCccccCCeEEEeEcCCCCceeccCCCc
Confidence 3678999999999995 67988888773334454 3343 589999999987 56788899999977553 36788
Q ss_pred eeEEEee---ecCChh
Q 027342 102 SRRVSLV---HYPEPK 114 (224)
Q Consensus 102 sRRVsLV---rypeP~ 114 (224)
.|-+.|. ..|...
T Consensus 80 ~~~~~I~e~~~ip~~~ 95 (198)
T PF08208_consen 80 DRFLHISEIVQIPQID 95 (198)
T ss_dssp SEEEEEEE--------
T ss_pred ceEEEEEEecCCCCcc
Confidence 8888886 455554
No 2
>TIGR02276 beta_rpt_yvtn 40-residue YVTN family beta-propeller repeat. This repeat of about 40 amino acids is found in up to 14 copies per protein. Archaea Methanosarcina mazei and Methanosarcina acetivorans each have over 10 genes that encode tandem copies of this repeat, which is also found in other species. PSIPRED predicts with high confidence that each 40-residue repeats contains four beta strands. This model overlaps somewhat with the NHL repeat (Pfam pfam01436) and also shows sequence similarity to the WD domain, G-beta repeat (Pfam pfam00400).
Probab=36.19 E-value=1e+02 Score=18.63 Aligned_cols=39 Identities=13% Similarity=0.192 Sum_probs=24.3
Q ss_pred CceeEEeecCCcceeeeecCCCCeeeeeeccCCCCCeeEE
Q 027342 49 GKELSLELRGNGRLGSFEDSSGKAYDIVSNDFQEPDEMVF 88 (224)
Q Consensus 49 G~~lslkl~~DG~Lg~Fe~SsGK~YdlVS~~aq~pdatvf 88 (224)
|++|-+...+++.|.-|-...++...-+.- ...|..++|
T Consensus 3 ~~~lyv~~~~~~~v~~id~~~~~~~~~i~v-g~~P~~i~~ 41 (42)
T TIGR02276 3 GTKLYVTNSGSNTVSVIDTATNKVIATIPV-GGYPFGVAV 41 (42)
T ss_pred CCEEEEEeCCCCEEEEEECCCCeEEEEEEC-CCCCceEEe
Confidence 777888877777777776555655555544 244555443
No 3
>PF15174 PRNT: Prion-related protein testis-specific
Probab=32.70 E-value=10 Score=27.44 Aligned_cols=11 Identities=36% Similarity=0.752 Sum_probs=9.6
Q ss_pred eeEEEecCCCC
Q 027342 33 ELWLIQWPYKQ 43 (224)
Q Consensus 33 ELWLIQ~P~~~ 43 (224)
.||++|+|.|-
T Consensus 29 SLW~LqiPvDc 39 (51)
T PF15174_consen 29 SLWHLQIPVDC 39 (51)
T ss_pred HHHhhcCCcch
Confidence 59999999875
No 4
>PF11197 DUF2835: Protein of unknown function (DUF2835); InterPro: IPR021363 This is a bacterial family of uncharacterised proteins. One member of this family (A4VM42 from SWISSPROT) is annotated as the A subunit of Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV).
Probab=30.55 E-value=40 Score=25.25 Aligned_cols=29 Identities=31% Similarity=0.658 Sum_probs=19.4
Q ss_pred EecCCCCC-----CC-CCCceeEEeecCCcceeeee
Q 027342 37 IQWPYKQM-----PD-FDGKELSLELRGNGRLGSFE 66 (224)
Q Consensus 37 IQ~P~~~~-----~D-f~G~~lslkl~~DG~Lg~Fe 66 (224)
||+|+..| .+ ++| .|.|..+++|+|-++|
T Consensus 33 v~~Pa~~lRpFvt~~Gv~G-~F~l~~d~~~kf~sle 67 (68)
T PF11197_consen 33 VQFPARHLRPFVTHDGVHG-RFRLEFDDNNKFVSLE 67 (68)
T ss_pred EEEeHHHCcceecCCCceE-EEEEEECCCCCEEEeE
Confidence 56798886 22 344 5777778888776654
No 5
>TIGR03352 VI_chp_3 type VI secretion lipoprotein, VC_A0113 family. Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (PubMed:16763151). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al.
Probab=30.42 E-value=83 Score=25.96 Aligned_cols=58 Identities=17% Similarity=0.321 Sum_probs=40.0
Q ss_pred cccCCCCCCCceeEEEecCCCCCCCCCCcee--EEeecCC----cceeeeecCCCCeeeeeeccCCCCCeeEEe
Q 027342 22 PLVDLSLIDSTELWLIQWPYKQMPDFDGKEL--SLELRGN----GRLGSFEDSSGKAYDIVSNDFQEPDEMVFL 89 (224)
Q Consensus 22 ~l~d~~ltDStELWLIQ~P~~~~~Df~G~~l--slkl~~D----G~Lg~Fe~SsGK~YdlVS~~aq~pdatvfv 89 (224)
..+.-++.+..|+.|. | |++. +++++.+ |+++.|-+-.+..|+++-.-.+..+-.+.|
T Consensus 76 ~~Lg~~ll~~~e~~l~--P--------G~~~~~~~~~~~~a~~igVvA~fr~~~~~~Wr~~~~~~~~~~~~~~v 139 (146)
T TIGR03352 76 KALGDDLIEQDEIILL--P--------GEKRKITITLDPGTRYIGVVAAYRDIDNAEWRVVYKVPPKGKYKIDV 139 (146)
T ss_pred HHHHHHHhhcceEEEC--C--------CCeeEeeeecCCCCeEEEEEEEeecCCCCceEEEEecCCCCceeEEE
Confidence 4456677778888654 4 4444 4444444 899999999999999988776655554443
No 6
>COG3338 Cah Carbonic anhydrase [Inorganic ion transport and metabolism]
Probab=27.86 E-value=47 Score=30.78 Aligned_cols=36 Identities=22% Similarity=0.516 Sum_probs=26.4
Q ss_pred CCCceeEEeecCCcceeeeecCCCCeeeeeeccCCCCCe
Q 027342 47 FDGKELSLELRGNGRLGSFEDSSGKAYDIVSNDFQEPDE 85 (224)
Q Consensus 47 f~G~~lslkl~~DG~Lg~Fe~SsGK~YdlVS~~aq~pda 85 (224)
.+|.+|.+....++..=.| +||.|.||+|++-.|.+
T Consensus 85 nnghTiqv~~~~~~n~l~~---~gk~y~L~qfHFH~PsE 120 (250)
T COG3338 85 NNGHTIQVNFEPGSNHLRY---DGKTYQLVQFHFHAPSE 120 (250)
T ss_pred ecCcEEEEeccCCCcceee---cCcEEEEEEEEecCchH
Confidence 5688888777766543332 69999999999886654
No 7
>PRK12694 flgG flagellar basal body rod protein FlgG; Reviewed
Probab=26.33 E-value=1.7e+02 Score=26.04 Aligned_cols=22 Identities=9% Similarity=0.288 Sum_probs=17.5
Q ss_pred EEEeeecCChhhhhccCCcccc
Q 027342 104 RVSLVHYPEPKEVEELNPDKIR 125 (224)
Q Consensus 104 RVsLVrypeP~Elek~~~~~~~ 125 (224)
|+.||.+++|..|++...+-.+
T Consensus 172 ~l~lv~~~~~~~L~~~G~~lf~ 193 (260)
T PRK12694 172 QLQLATFINPAGLQAKGENLFA 193 (260)
T ss_pred eeEEEecCChHhCeEcCCCceE
Confidence 5789999999999997655443
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=26.23 E-value=1.6e+02 Score=21.97 Aligned_cols=31 Identities=10% Similarity=0.231 Sum_probs=24.0
Q ss_pred CCCCCceeEEEecCCCCCCCCCCceeEEeecCCc
Q 027342 27 SLIDSTELWLIQWPYKQMPDFDGKELSLELRGNG 60 (224)
Q Consensus 27 ~ltDStELWLIQ~P~~~~~Df~G~~lslkl~~DG 60 (224)
|..+..+=|.|.+ .+|.|....|.|+.+++-
T Consensus 2 ~v~e~~~~~~v~~---dlpG~~pedi~V~v~~~~ 32 (81)
T cd06479 2 NVKTLGDTYQFAV---DVSDFSPEDIIVTTSNNQ 32 (81)
T ss_pred CccCcCCeEEEEE---ECCCCCHHHeEEEEECCE
Confidence 4566778888875 368888999999998764
No 9
>PTZ00363 rab-GDP dissociation inhibitor; Provisional
Probab=25.11 E-value=2e+02 Score=27.64 Aligned_cols=21 Identities=33% Similarity=0.570 Sum_probs=17.7
Q ss_pred cccceeeeEEEeeecCChhhh
Q 027342 96 KIVGKISRRVSLVHYPEPKEV 116 (224)
Q Consensus 96 ~ivgKIsRRVsLVrypeP~El 116 (224)
+-+|+|.|-||++.-|-|+--
T Consensus 294 ~~~~~v~R~i~i~~~pi~~~~ 314 (443)
T PTZ00363 294 KKVGKVIRCICILNHPIPNTN 314 (443)
T ss_pred ccccEEEEEEEEEcccccccC
Confidence 458999999999999987743
No 10
>PRK12691 flgG flagellar basal body rod protein FlgG; Reviewed
Probab=24.53 E-value=1.6e+02 Score=26.00 Aligned_cols=22 Identities=14% Similarity=0.439 Sum_probs=17.6
Q ss_pred EEEeeecCChhhhhccCCcccc
Q 027342 104 RVSLVHYPEPKEVEELNPDKIR 125 (224)
Q Consensus 104 RVsLVrypeP~Elek~~~~~~~ 125 (224)
+|.||.+++|..|++..-+-.+
T Consensus 172 ~l~lv~~~~~~~L~~~g~~lf~ 193 (262)
T PRK12691 172 QITLARFTNEAGLEAIGDNLFR 193 (262)
T ss_pred eeEEEecCChHHCeECCCCeEE
Confidence 5789999999999986655443
No 11
>PRK12819 flgG flagellar basal body rod protein FlgG; Reviewed
Probab=24.51 E-value=90 Score=27.69 Aligned_cols=26 Identities=4% Similarity=0.128 Sum_probs=19.7
Q ss_pred ccceeeeEEEeeecCChhhhhccCCccc
Q 027342 97 IVGKISRRVSLVHYPEPKEVEELNPDKI 124 (224)
Q Consensus 97 ivgKIsRRVsLVrypeP~Elek~~~~~~ 124 (224)
.+|+| +|.||.+|+|..|++..-+-.
T Consensus 166 ~vg~l--~l~~v~~~~~~~L~~~g~~lf 191 (257)
T PRK12819 166 NIARL--QTKTVSAEQNDRLVQRENKSF 191 (257)
T ss_pred eEEEE--EEEEeCCCCHHHCeECCCCeE
Confidence 36666 566799999999999665544
No 12
>PF11720 Inhibitor_I78: Peptidase inhibitor I78 family; InterPro: IPR021719 This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78.
Probab=23.72 E-value=1.8e+02 Score=20.58 Aligned_cols=20 Identities=20% Similarity=0.444 Sum_probs=18.3
Q ss_pred CCCCCceeEEeecCCcceee
Q 027342 45 PDFDGKELSLELRGNGRLGS 64 (224)
Q Consensus 45 ~Df~G~~lslkl~~DG~Lg~ 64 (224)
-||+..+|.|.++.+|+|-.
T Consensus 37 mDyr~dRLnv~~D~~g~I~~ 56 (60)
T PF11720_consen 37 MDYRPDRLNVEVDDDGVITR 56 (60)
T ss_pred ccCCCCcEEEEECCCCcEEE
Confidence 89999999999999998754
No 13
>PF04435 SPK: Domain of unknown function (DUF545) ; InterPro: IPR006570 SPK is a domain of unknown function found in SET and PHD domain containing proteins and protein kinases.
Probab=23.17 E-value=19 Score=26.89 Aligned_cols=38 Identities=18% Similarity=0.450 Sum_probs=27.4
Q ss_pred eeEEEecCCCC-C-CCCCCceeEEeecCCcceeeeecCCCC
Q 027342 33 ELWLIQWPYKQ-M-PDFDGKELSLELRGNGRLGSFEDSSGK 71 (224)
Q Consensus 33 ELWLIQ~P~~~-~-~Df~G~~lslkl~~DG~Lg~Fe~SsGK 71 (224)
=+|..++|++. | ..++- .-.|++|..|+|-.|++-+|+
T Consensus 67 m~F~l~~pV~~~fl~~L~~-~a~v~lD~~~rI~~Y~s~dg~ 106 (109)
T PF04435_consen 67 MLFALSIPVDEEFLKELRK-HADVELDEKGRIIKYKSKDGS 106 (109)
T ss_pred HHHHcCCCcCHHHHHHHHh-CcEEEEcCCCCEEEEEeCCCE
Confidence 47899999987 2 33322 223888999999999977774
No 14
>PRK12693 flgG flagellar basal body rod protein FlgG; Provisional
Probab=22.96 E-value=1.8e+02 Score=25.58 Aligned_cols=22 Identities=14% Similarity=0.392 Sum_probs=17.2
Q ss_pred EEEeeecCChhhhhccCCcccc
Q 027342 104 RVSLVHYPEPKEVEELNPDKIR 125 (224)
Q Consensus 104 RVsLVrypeP~Elek~~~~~~~ 125 (224)
||.||.+++|..|++..-+-.+
T Consensus 172 ~l~~~~~~~~~~L~~~g~~lf~ 193 (261)
T PRK12693 172 QITLTDFINPAGLESIGENLYL 193 (261)
T ss_pred ceeEEecCChHHceECCCceEE
Confidence 4789999999999996655443
No 15
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=22.91 E-value=46 Score=23.72 Aligned_cols=37 Identities=16% Similarity=0.316 Sum_probs=25.5
Q ss_pred CCCCCCCCCCceeEEeecCC----cceeeeecCCCCeeeeeeccC
Q 027342 40 PYKQMPDFDGKELSLELRGN----GRLGSFEDSSGKAYDIVSNDF 80 (224)
Q Consensus 40 P~~~~~Df~G~~lslkl~~D----G~Lg~Fe~SsGK~YdlVS~~a 80 (224)
|++.+..+-|++++|++.++ |.|-+|. .-..|+=..|
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D----~~mNlvL~~~ 41 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLD----GYMNIALEQT 41 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEc----cceeeEEeeE
Confidence 56667778899999999975 6666655 2445555443
Done!