Query 000637
Match_columns 1378
No_of_seqs 252 out of 363
Neff 3.1
Searched_HMMs 29240
Date Tue Mar 26 17:47:26 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000637.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_408-412//hhsearch_pdb/000637hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2e70_A Transcription elongatio 1.0 1 1 148.6 8.8 55 245-299 15-69 (71)
2 2e6z_A Transcription elongatio 1.0 1 1 40.7 5.8 49 247-295 7-57 (59)
3 2ckk_A KIN17; beta barrel, rib 1.0 1 1 40.0 11.8 104 140-296 11-125 (127)
4 3iz5_Y 60S ribosomal protein L 1.0 1 1 37.5 2.1 30 142-171 47-76 (150)
5 1nz9_A Transcription antitermi 1.0 1 1 37.2 5.8 45 248-292 5-51 (58)
6 3p8b_B Transcription antitermi 1.0 1 1 37.0 7.0 52 247-298 91-146 (152)
7 2jvv_A Transcription antitermi 1.0 1 1 36.2 5.9 46 247-292 127-174 (181)
8 2zkr_t 60S ribosomal protein L 1.0 1 1 35.8 3.9 35 142-176 47-82 (145)
9 1vq8_T 50S ribosomal protein L 1.0 1 1 35.3 4.0 30 142-171 41-70 (120)
10 3r8s_U 50S ribosomal protein L 1.0 1 1 35.3 5.0 29 142-170 2-30 (102)
No 1
>2e70_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=148.62 Aligned_cols=55 Identities=33% Similarity=0.447 Sum_probs=51.5
Q ss_pred CCCCCCCCEEEEECCCCCCCEEEEEEECCCEEEEEECCCCEEEEEECCCCEECCC
Q ss_conf 8863357589990279987215999651983899945776199980775100147
Q 000637 245 DGMFAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEVRG 299 (1378)
Q Consensus 245 d~D~LIGKTVKIRkGPYKGYlGiVKDvTdt~VRVELHSK~KtVTVdKe~Lsvv~g 299 (1378)
++|+||||||+|++||||||+|||||+|+++||||||++||+|+|+|++|.+++.
T Consensus 15 grd~liGktV~I~kGpyKG~~GiVkd~t~~~~RVELhs~~K~VtV~r~~l~~~~~ 69 (71)
T 2e70_A 15 RDNELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLTTVGS 69 (71)
T ss_dssp CTTSSTTSEEEECSSTTTTCEEEEEEECSSCEEEEESSSCCEEEECTTTEEECCC
T ss_pred CCCCCCCCEEEEECCCCCCEEEEEEECCCCEEEEEECCCCEEEEEEHHHCCCCCC
T ss_conf 7654589788994268888378899778986999956886699988555413687
No 2
>2e6z_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=40.66 Aligned_cols=49 Identities=18% Similarity=0.309 Sum_probs=39.7
Q ss_pred CCCCCCEEEEECCCCCCCEEEEEEECCCEEEEEEC--CCCEEEEEECCCCE
Q ss_conf 63357589990279987215999651983899945--77619998077510
Q 000637 247 MFAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLD--SQQKILTVKGEHLA 295 (1378)
Q Consensus 247 D~LIGKTVKIRkGPYKGYlGiVKDvTdt~VRVELH--SK~KtVTVdKe~Ls 295 (1378)
++.+|.+|+|+.||++|+.|+|.++....++|.|. -....|.|+-..|.
T Consensus 7 ~f~~GD~V~V~~Gpf~g~~G~V~evd~e~v~V~v~~fg~~tpvel~~~qv~ 57 (59)
T 2e6z_A 7 GFQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDMLEFPAQELR 57 (59)
T ss_dssp SCCTTSEEEECSSTTTTCEEEECCCBTTEEEEEECCSSCCSCEEEETTTEE
T ss_pred CCCCCCEEEEEECCCCCCEEEEEEEECCEEEEEEEECCCCCEEEECHHHEE
T ss_conf 679999999925588997999999969999999981688836997088989
No 3
>2ckk_A KIN17; beta barrel, ribosomal protein, ribonucleoprotein, nuclear protein; 1.45A {Homo sapiens}
Probab=1.00 E-value=1 Score=40.02 Aligned_cols=104 Identities=12% Similarity=0.165 Sum_probs=73.0
Q ss_pred CCCEECCCCEEEEECCC----CCCCEEEEEEEECC-EEEEEECCCCCCCCEEEEECCCEEECCCCCCCCCCCCCCCCCCC
Q ss_conf 99942269959991599----98861589999923-69998054222462899928945660332225889999999998
Q 000637 140 SMKVISLNDTARVSEGP----SKDRQGIVKKIYRG-ILFIYDENETENGGYFCSKSQHCEKTKVEACEGKGGGSGASGFE 214 (1378)
Q Consensus 140 nGNtIsVGDtVKVVdGP----~KGRQG~VlHIyRg-~LFL~sR~i~ENgGIFVvrArnVvlVGg~as~sK~g~ss~~~l~ 214 (1378)
...=+..+=+|||++-. |-++.|+|+-+-.. .+-|+. .+++-++-+...++++|-
T Consensus 11 ~~~Wl~~~I~Vrii~k~~~~g~y~~KgvV~~V~~~~~c~V~l---~~~g~~v~v~q~~LETVi----------------- 70 (127)
T 2ckk_A 11 TDYWLQPEIIVKIITKKLGEKYHKKKAIVKEVIDKYTAVVKM---IDSGDKLKLDQTHLETVI----------------- 70 (127)
T ss_dssp CSCCCCTTBEEEECCSTTCGGGTTCEEEEEEEETTTEEEEEE---TTTCCEEEEEGGGEEECC-----------------
T ss_pred CCCCCCCCEEEEEEECCCCCCCCCCEEEEEEECCCCEEEEEE---CCCCCEEEECHHHCEEEC-----------------
T ss_conf 888530986999997667875137408999966898199997---799979987369928843-----------------
Q ss_pred CCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCEEEEEEECCC--EEEEEECCC---CEEE-E
Q ss_conf 899999999999651000026877878888886335758999027998721599965198--389994577---6199-9
Q 000637 215 EFPSSPKSPLSPKRSWQAREQNTEFKRGDRDGMFAVGQTLRIRVGPLKGYLCRVLAVRYS--DVTVKLDSQ---QKIL-T 288 (1378)
Q Consensus 215 dl~sSp~splSP~rp~q~rg~~r~fgRGGRd~D~LIGKTVKIRkGPYKGYlGiVKDvTdt--~VRVELHSK---~KtV-T 288 (1378)
|.+|..|+|..|+|+|..|+++.+... .|.|+|.+. .++| .
T Consensus 71 ---------------------------------P~~g~~V~Iv~G~~rG~~g~L~~id~~~~~~~V~l~~~~~~~~~v~~ 117 (127)
T 2ckk_A 71 ---------------------------------PAPGKRILVLNGGYRGNEGTLESINEKTFSATIVIETGPLKGRRVEG 117 (127)
T ss_dssp ---------------------------------CCTTCEEEECSSTTTTCEEEEEEEEGGGTEEEEEECSSTTTTCEEEE
T ss_pred ---------------------------------CCCCCEEEEEECCCCCCEEEEEEEECCCCEEEEEECCCCCCCCEEEE
T ss_conf ---------------------------------78999899984465784899999968776899998668878879975
Q ss_pred EECCCCEE
Q ss_conf 80775100
Q 000637 289 VKGEHLAE 296 (1378)
Q Consensus 289 VdKe~Lsv 296 (1378)
++-++|..
T Consensus 118 l~~ddi~k 125 (127)
T 2ckk_A 118 IQYEDISK 125 (127)
T ss_dssp EEGGGEEE
T ss_pred ECHHHHHC
T ss_conf 48999404
No 4
>3iz5_Y 60S ribosomal protein L26 (L24P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} PDB: 3izr_Y
Probab=1.00 E-value=1 Score=37.50 Aligned_cols=30 Identities=33% Similarity=0.486 Sum_probs=27.4
Q ss_pred CEECCCCEEEEECCCCCCCEEEEEEEECCE
Q ss_conf 942269959991599988615899999236
Q 000637 142 KVISLNDTARVSEGPSKDRQGIVKKIYRGI 171 (1378)
Q Consensus 142 NtIsVGDtVKVVdGP~KGRQG~VlHIyRg~ 171 (1378)
-.|+.+|+|+||.|.++|++|.|+.||+-.
T Consensus 47 ~~IkKGD~V~Vi~GkdKGk~GkVl~V~~kk 76 (150)
T 3iz5_Y 47 IPIRKDDEVQVVRGSYKGREGKVVQVYRRR 76 (150)
T ss_dssp EECCSSSEEEECSSTTTTCEEEEEEEETTT
T ss_pred CCCCCCCEEEEEECCCCCCCCEEEEEECCC
T ss_conf 442799999981548999534488997678
No 5
>1nz9_A Transcription antitermination protein NUSG; transcription elongation, riken structural genomics/proteomics initiative, RSGI; NMR {Thermus thermophilus} SCOP: b.34.5.4
Probab=1.00 E-value=1 Score=37.24 Aligned_cols=45 Identities=20% Similarity=0.319 Sum_probs=36.8
Q ss_pred CCCCCEEEEECCCCCCCEEEEEEECCC--EEEEEECCCCEEEEEECC
Q ss_conf 335758999027998721599965198--389994577619998077
Q 000637 248 FAVGQTLRIRVGPLKGYLCRVLAVRYS--DVTVKLDSQQKILTVKGE 292 (1378)
Q Consensus 248 ~LIGKTVKIRkGPYKGYlGiVKDvTdt--~VRVELHSK~KtVTVdKe 292 (1378)
.-+|.+|+|+.|||+|+.|+|.++... .++|+|..-.+.+.|+-+
T Consensus 5 ~~~Gd~V~V~~Gpf~g~~g~v~~v~~~k~~v~V~v~~~Gr~t~v~l~ 51 (58)
T 1nz9_A 5 FREGDQVRVVSGPFADFTGTVTEINPERGKVKVMVTIFGRETPVELD 51 (58)
T ss_dssp CCTTCEEEECSGGGTTCEEEEEEEETTTTEEEEEEESSSSEEEEEEC
T ss_pred CCCCCEEEEEECCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEEC
T ss_conf 58999999951689996999999818789999999957998999988
No 6
>3p8b_B Transcription antitermination protein NUSG; transcription elongation factor, RNA polymerase, transferase transcription complex; 1.80A {Pyrococcus furiosus} PDB: 3qqc_D
Probab=1.00 E-value=1 Score=37.04 Aligned_cols=52 Identities=23% Similarity=0.390 Sum_probs=42.0
Q ss_pred CCCCCCEEEEECCCCCCCEEEEEEECCC--EEEEEECCCCE--EEEEECCCCEECC
Q ss_conf 6335758999027998721599965198--38999457761--9998077510014
Q 000637 247 MFAVGQTLRIRVGPLKGYLCRVLAVRYS--DVTVKLDSQQK--ILTVKGEHLAEVR 298 (1378)
Q Consensus 247 D~LIGKTVKIRkGPYKGYlGiVKDvTdt--~VRVELHSK~K--tVTVdKe~Lsvv~ 298 (1378)
+..+|.+|+|+.|||+|+.|+|.+++.. .|+|+|..-.+ .|+|+-+.|..+.
T Consensus 91 ~~~~Gd~VrI~~Gpf~g~~g~V~~vd~~k~~v~V~v~~~gr~tpvel~~~~v~~i~ 146 (152)
T 3p8b_B 91 GLEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQFIDAIVPIPVTIKGDYVRLIS 146 (152)
T ss_dssp TCCTTCEEEECSSTTTTCEEEEEEEETTTTEEEEEESSCSSCCEEEEEGGGEEEEE
T ss_pred CCCCCCEEEEEEECCCCCEEEEEEEECCCCEEEEEEEECCEEEEEEECHHHEEEEC
T ss_conf 67789999994405899789999992898899999993363689998779989913
No 7
>2jvv_A Transcription antitermination protein NUSG; transcription factor, transcription regulation, transcription termination; NMR {Escherichia coli} PDB: 2k06_A 2kvq_G
Probab=1.00 E-value=1 Score=36.23 Aligned_cols=46 Identities=22% Similarity=0.393 Sum_probs=37.2
Q ss_pred CCCCCCEEEEECCCCCCCEEEEEEECCC--EEEEEECCCCEEEEEECC
Q ss_conf 6335758999027998721599965198--389994577619998077
Q 000637 247 MFAVGQTLRIRVGPLKGYLCRVLAVRYS--DVTVKLDSQQKILTVKGE 292 (1378)
Q Consensus 247 D~LIGKTVKIRkGPYKGYlGiVKDvTdt--~VRVELHSK~KtVTVdKe 292 (1378)
+..+|.+|+|+.|||+|+.|+|.++... .++|+|..-.+.+.|.-+
T Consensus 127 ~~~~Gd~V~V~~GPf~g~~G~v~~v~~~k~r~~V~v~ifgr~t~vel~ 174 (181)
T 2jvv_A 127 LFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELD 174 (181)
T ss_dssp CCCTTEEEEECSSTTTTEEEEEEEEETTTTEEEEEEEETTEEEEEEEC
T ss_pred CCCCCCEEEEECCCCCCCEEEEEEEECCCCEEEEEEEECCCCEEEEEC
T ss_conf 689999999954578996899999948999999999977997799988
No 8
>2zkr_t 60S ribosomal protein L26; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}
Probab=1.00 E-value=1 Score=35.82 Aligned_cols=35 Identities=34% Similarity=0.468 Sum_probs=29.1
Q ss_pred CEECCCCEEEEECCCCCCCE-EEEEEEECCEEEEEE
Q ss_conf 94226995999159998861-589999923699980
Q 000637 142 KVISLNDTARVSEGPSKDRQ-GIVKKIYRGILFIYD 176 (1378)
Q Consensus 142 NtIsVGDtVKVVdGP~KGRQ-G~VlHIyRg~LFL~s 176 (1378)
-.|+.+|+|.||.|+++|++ |.|+.|++..-.|+.
T Consensus 47 ~~IkkGD~V~Vi~GkdKGk~~GkV~~V~~k~~~V~V 82 (145)
T 2zkr_t 47 MPIRKDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYI 82 (145)
T ss_dssp CBCCTTCEEEECSSTTTTCCSEEEEEEETTTTEEEE
T ss_pred CCCCCCCEEEEEECCCCCCCEEEEEEEECCCCEEEE
T ss_conf 651799999983468899320299999888999999
No 9
>1vq8_T 50S ribosomal protein L24P; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: b.34.5.1 PDB: 1vq4_T* 1vq5_T* 1vq6_T* 1vq7_T* 1s72_T* 1vq9_T* 1vqk_T* 1vql_T* 1vqm_T* 1vqn_T* 1vqo_T* 1vqp_T* 1yhq_T* 1yi2_T* 1yij_T* 1yit_T* 1yj9_T* 1yjn_T* 1yjw_T* 2otj_T* ...
Probab=1.00 E-value=1 Score=35.33 Aligned_cols=30 Identities=20% Similarity=0.179 Sum_probs=26.5
Q ss_pred CEECCCCEEEEECCCCCCCEEEEEEEECCE
Q ss_conf 942269959991599988615899999236
Q 000637 142 KVISLNDTARVSEGPSKDRQGIVKKIYRGI 171 (1378)
Q Consensus 142 NtIsVGDtVKVVdGP~KGRQG~VlHIyRg~ 171 (1378)
-.|+.+|+|.||.|+++|++|.|+.||+..
T Consensus 41 ~~IkkGD~V~Vi~G~dKGk~GkV~~V~~k~ 70 (120)
T 1vq8_T 41 VRVNAGDTVEVLRGDFAGEEGEVINVDLDK 70 (120)
T ss_dssp EECCTTCEEEECSSTTTTCEEEEEEEETTT
T ss_pred CCCCCCCEEEEEECCCCCCEEEEEEEECCC
T ss_conf 540699999997438899778999998889
No 10
>3r8s_U 50S ribosomal protein L24; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 2j28_U* 3fik_U 3j19_U 2wwq_U 3oat_U* 3oas_U* 3ofd_U 3ofc_U 3ofr_U* 3ofz_U* 3og0_U 3ofq_U 3r8t_U 3i1n_U 1vs8_U 1vs6_U 1vt2_U 3i1p_U 3i1r_U 3i1t_U ...
Probab=1.00 E-value=1 Score=35.31 Aligned_cols=29 Identities=28% Similarity=0.397 Sum_probs=27.1
Q ss_pred CEECCCCEEEEECCCCCCCEEEEEEEECC
Q ss_conf 94226995999159998861589999923
Q 000637 142 KVISLNDTARVSEGPSKDRQGIVKKIYRG 170 (1378)
Q Consensus 142 NtIsVGDtVKVVdGP~KGRQG~VlHIyRg 170 (1378)
.-|+.+|+|.||.|.++|++|.|+.||+.
T Consensus 2 ~~IkkGD~V~Vi~GkdKGk~GkV~~V~~~ 30 (102)
T 3r8s_U 2 AKIRRDDEVIVLTGKDKGKRGKVKNVLSS 30 (102)
T ss_dssp CSSCSSCEEEECSSSSTTCEEEEEEEETT
T ss_pred CCCCCCCEEEEEECCCCCEEEEEEEEEEC
T ss_conf 97669999999585999906689999719
Done!