Align Dihydrolipoyl dehydrogenase, mitochondrial; Dihydrolipoamide dehydrogenase; Glycine cleavage system L protein; Pyruvate dehydrogenase complex E3 subunit; E3; PDC-E3; EC 1.8.1.4 (characterized)
to candidate AZOBR_RS03960 AZOBR_RS03960 dihydrolipoamide dehydrogenase
Query= SwissProt::P31023 (501 letters) >FitnessBrowser__azobra:AZOBR_RS03960 Length = 466 Score = 579 bits (1492), Expect = e-170 Identities = 283/463 (61%), Positives = 349/463 (75%), Gaps = 3/463 (0%) Query: 39 DVVIIGGGPGGYVAAIKAAQLGFKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 98 DVV++GGGPGGYV AI+AAQLGFK C+EKR ALGGTCLNVGCIPSKALL +S Y EAK Sbjct: 7 DVVVVGGGPGGYVCAIRAAQLGFKVACVEKRSALGGTCLNVGCIPSKALLAASEKYEEAK 66 Query: 99 HSFANHGVKVSNVEIDLAAMMGQKDKAVSNLTRGIEGLFKKNKVTYVKGYGKFVSPSEIS 158 H A G+KV VE+DL M+ KDK V T GIE LFKKNK+ ++KG G+ +P+ + Sbjct: 67 HGLAKFGIKVDGVELDLPGMLSHKDKVVKENTGGIEFLFKKNKIAWLKGAGRITAPNTVE 126 Query: 159 VDTIEGENTVVKGKHIIIATGSDVKSLPGVTIDEKKIVSSTGALALSEIPKKLVVIGAGY 218 V EG T+ K I+IATGS+V LPG+ IDE+KIVSSTGAL L E+PK+LVVIG G Sbjct: 127 V---EGVGTITASKAIVIATGSEVTPLPGIEIDEQKIVSSTGALELPEVPKRLVVIGGGV 183 Query: 219 IGLEMGSVWGRIGSEVTVVEFASEIVPTMDAEIRKQFQRSLEKQGMKFKLKTKVVGVDTS 278 IGLE+GSVWGR+G+EVTVVEF I+PTMD E+ KQ QR L KQGM FKL +KV G + Sbjct: 184 IGLELGSVWGRLGAEVTVVEFLDRILPTMDGEVSKQMQRILGKQGMTFKLGSKVTGAKVT 243 Query: 279 GDGVKLTVEPSAGGEQTIIEADVVLVSAGRTPFTSGLNLDKIGVETDKLGRILVNERFST 338 GV L+VEP+AGG I+ADVVLV+ GR FT+GL LD +GVE D GR+ + + F T Sbjct: 244 NTGVTLSVEPAAGGTAEEIKADVVLVAIGRRAFTNGLGLDAVGVEMDNRGRVKIGKHFET 303 Query: 339 NVSGVYAIGDVIPGPMLAHKAEEDGVACVEYLAGKVGHVDYDKVPGVVYTNPEVASVGKT 398 NV G+YAIGDV+ GPMLAHKAEE+GVA E LAG+ GHV++D VPGVVYT PEVA+VGKT Sbjct: 304 NVPGIYAIGDVVEGPMLAHKAEEEGVALAELLAGQAGHVNHDLVPGVVYTWPEVAAVGKT 363 Query: 399 EEQVKETGVEYRVGKFPFMANSRAKAIDNAEGLVKIIAEKETDKILGVHIMAPNAGELIH 458 EE++K G Y+ GKFPF AN RA+A +G VKI+A+ TDK+LGVH++ PN E++ Sbjct: 364 EEELKAAGTAYKAGKFPFTANGRARASGTTDGFVKILADARTDKVLGVHMVGPNVSEMVA 423 Query: 459 EAAIALQYDASSEDIARVCHAHPTMSEAIKEAAMATYDKPIHI 501 E A+A+++ AS+EDIAR CHAHPT+SE KEAA+A + +HI Sbjct: 424 ELAVAMEFSASAEDIARTCHAHPTLSEVTKEAALAVDGRALHI 466 Lambda K H 0.315 0.133 0.370 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 715 Number of extensions: 31 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 501 Length of database: 466 Length adjustment: 34 Effective length of query: 467 Effective length of database: 432 Effective search space: 201744 Effective search space used: 201744 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 52 (24.6 bits)
Align candidate AZOBR_RS03960 AZOBR_RS03960 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR01350.hmm # target sequence database: /tmp/gapView.28281.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01350 [M=461] Accession: TIGR01350 Description: lipoamide_DH: dihydrolipoyl dehydrogenase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-180 586.2 11.0 2.5e-180 586.0 11.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS03960 AZOBR_RS03960 dihydrolipoamide d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS03960 AZOBR_RS03960 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 586.0 11.0 2.5e-180 2.5e-180 2 461 .] 6 466 .] 5 466 .] 0.97 Alignments for each domain: == domain 1 score: 586.0 bits; conditional E-value: 2.5e-180 TIGR01350 2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgi 68 +dvvv+GgGpgGYv+Airaaqlg+kva+vek + lGGtClnvGCiP+KalL+++e +ee+k+ ++++gi lcl|FitnessBrowser__azobra:AZOBR_RS03960 6 FDVVVVGGGPGGYVCAIRAAQLGFKVACVEKrSALGGTCLNVGCIPSKALLAASEKYEEAKHgLAKFGI 74 8******************************899*********************************** PP TIGR01350 69 evenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniii 137 +v++v+ldl +l +k+kvvk+ +gG+++L+kknk+ +kG ++++ +++vev++ + k+i+i lcl|FitnessBrowser__azobra:AZOBR_RS03960 75 KVDGVELDLPGMLSHKDKVVKENTGGIEFLFKKNKIAWLKGAGRITAPNTVEVEGVG--TITASKAIVI 141 *******************************************************98..4678999*** PP TIGR01350 138 AtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldril 206 AtGse++ lp+ +e de+ +++s++alel+evp++lv++GgGviG+E++s++ +lG++vtv+e+ldril lcl|FitnessBrowser__azobra:AZOBR_RS03960 142 ATGSEVTPLPG-IEIDEQKIVSSTGALELPEVPKRLVVIGGGVIGLELGSVWGRLGAEVTVVEFLDRIL 209 ***********.********************************************************* PP TIGR01350 207 paldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnle 272 p++d evsk++++ l k+g++++ ++kvt + ++ v+ ve + ++e+++a+ vLva+Gr++ ++ lcl|FitnessBrowser__azobra:AZOBR_RS03960 210 PTMDGEVSKQMQRILGKQGMTFKLGSKVTGAKVTNTGVTlsVEPAAGgTAEEIKADVVLVAIGRRAFTN 278 *****************************666666666644666655699******************* PP TIGR01350 273 elgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidyka 341 +lgl+++gve+d+rg++k+ ++++tnvpgiyaiGDv++++mLAh+A++egv ae +ag++ ++++++ lcl|FitnessBrowser__azobra:AZOBR_RS03960 279 GLGLDAVGVEMDNRGRVKIGKHFETNVPGIYAIGDVVEGPMLAHKAEEEGVALAELLAGQAG-HVNHDL 346 ***********************************************************998.9***** PP TIGR01350 342 vPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivg 410 vP v+yt Peva+vG+tee++k++g+++k+gkfpf+ang+a+a++ tdGfvk+++d t+++lG+h+vg lcl|FitnessBrowser__azobra:AZOBR_RS03960 347 VPGVVYTWPEVAAVGKTEEELKAAGTAYKAGKFPFTANGRARASGTTDGFVKILADARTDKVLGVHMVG 415 ********************************************************************* PP TIGR01350 411 aeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461 +++se+++ela+a+e+ +++e++a+t+h+HPtlsE++keaala+ g+a+h+ lcl|FitnessBrowser__azobra:AZOBR_RS03960 416 PNVSEMVAELAVAMEFSASAEDIARTCHAHPTLSEVTKEAALAVDGRALHI 466 ***********************************************9995 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (466 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.49 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory