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 WP_011386317.1 AMB_RS20050 dihydrolipoyl dehydrogenase
Query= SwissProt::P31023 (501 letters) >NCBI__GCF_000009985.1:WP_011386317.1 Length = 469 Score = 580 bits (1496), Expect = e-170 Identities = 285/462 (61%), Positives = 352/462 (76%) Query: 39 DVVIIGGGPGGYVAAIKAAQLGFKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 98 DVVIIGGGPGGYVAAI+AAQLG KT CIEKRG+LGGTCLNVGCIPSKALL +SH YH A Sbjct: 7 DVVIIGGGPGGYVAAIRAAQLGLKTACIEKRGSLGGTCLNVGCIPSKALLTASHHYHAAA 66 Query: 99 HSFANHGVKVSNVEIDLAAMMGQKDKAVSNLTRGIEGLFKKNKVTYVKGYGKFVSPSEIS 158 H + G+KV+ VE+D+A MMG KDK VS+ T+GIE LFKKNKVTY+ G G +P +I Sbjct: 67 HELGSFGIKVAKVEMDVAGMMGHKDKVVSDNTKGIEFLFKKNKVTYIVGAGAITAPGQIE 126 Query: 159 VDTIEGENTVVKGKHIIIATGSDVKSLPGVTIDEKKIVSSTGALALSEIPKKLVVIGAGY 218 V +G + V KHI+IATGSDV LPGV IDE+ I+SSTGALALS+ PK +VVIG G Sbjct: 127 VTAKDGAKSNVAAKHIVIATGSDVTPLPGVEIDEEVIISSTGALALSKTPKHMVVIGGGV 186 Query: 219 IGLEMGSVWGRIGSEVTVVEFASEIVPTMDAEIRKQFQRSLEKQGMKFKLKTKVVGVDTS 278 IGLE+G+VWGR+G++VTVVEF I+P D E+ KQ QR L KQGM+FKL TKV G+ Sbjct: 187 IGLELGTVWGRLGAKVTVVEFLDRILPFNDGEVSKQMQRLLAKQGMEFKLGTKVTGIAKK 246 Query: 279 GDGVKLTVEPSAGGEQTIIEADVVLVSAGRTPFTSGLNLDKIGVETDKLGRILVNERFST 338 G +TVEP+AGG IEAD VLV+ GR P+T GL LDK+GV DK G + ++ F T Sbjct: 247 GKTATVTVEPAAGGAAEKIEADSVLVAIGRKPYTEGLGLDKVGVALDKRGFVQIDGHFRT 306 Query: 339 NVSGVYAIGDVIPGPMLAHKAEEDGVACVEYLAGKVGHVDYDKVPGVVYTNPEVASVGKT 398 NV G+YAIGDV+ G MLAHKAEE+GVA E LAG+ GHV+Y+ +P VVYT PEVASVGKT Sbjct: 307 NVPGIYAIGDVVGGAMLAHKAEEEGVALAEILAGQHGHVNYEAIPAVVYTWPEVASVGKT 366 Query: 399 EEQVKETGVEYRVGKFPFMANSRAKAIDNAEGLVKIIAEKETDKILGVHIMAPNAGELIH 458 EEQ+K G+ Y+ GKFPF AN RA++++ +G VK++A TDK+LG HI+ PNAG+LI Sbjct: 367 EEQLKAEGIAYKAGKFPFTANGRARSMNEVDGFVKVLACATTDKVLGAHIVGPNAGDLIA 426 Query: 459 EAAIALQYDASSEDIARVCHAHPTMSEAIKEAAMATYDKPIH 500 E +A+++ A+SEDIAR CHAHP + EA+KEA +A +P+H Sbjct: 427 EVVLAMEFGAASEDIARTCHAHPGLGEAVKEACLAVDGRPLH 468 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: 719 Number of extensions: 27 Number of successful extensions: 1 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: 469 Length adjustment: 34 Effective length of query: 467 Effective length of database: 435 Effective search space: 203145 Effective search space used: 203145 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 WP_011386317.1 AMB_RS20050 (dihydrolipoyl 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.10105.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-181 589.6 14.4 2.3e-181 589.4 14.4 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011386317.1 AMB_RS20050 dihydrolipoyl dehydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011386317.1 AMB_RS20050 dihydrolipoyl dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 589.4 14.4 2.3e-181 2.3e-181 2 460 .. 6 468 .. 5 469 .] 0.97 Alignments for each domain: == domain 1 score: 589.4 bits; conditional E-value: 2.3e-181 TIGR01350 2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgi 68 +dvv+iGgGpgGYvaAiraaqlglk+a++ek +lGGtClnvGCiP+KalL++++ ++ + + + ++gi lcl|NCBI__GCF_000009985.1:WP_011386317.1 6 FDVVIIGGGPGGYVAAIRAAQLGLKTACIEKrGSLGGTCLNVGCIPSKALLTASHHYHAAAHeLGSFGI 74 9******************************889****************************9****** PP TIGR01350 69 evenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleaknii 136 +v++v++d++ ++ +k+kvv+ ++G+++L+kknkv+ i G + ++ ++++ev++++++ +++ ak+i+ lcl|NCBI__GCF_000009985.1:WP_011386317.1 75 KVAKVEMDVAGMMGHKDKVVSDNTKGIEFLFKKNKVTYIVGAGAITAPGQIEVTAKDGAkSNVAAKHIV 143 *******************************************************998868899***** PP TIGR01350 137 iAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldri 205 iAtGs+++ lp+ +e de+v+i+s++al+l+++p+++v++GgGviG+E+++++ +lG+kvtv+e+ldri lcl|NCBI__GCF_000009985.1:WP_011386317.1 144 IATGSDVTPLPG-VEIDEEVIISSTGALALSKTPKHMVVIGGGVIGLELGTVWGRLGAKVTVVEFLDRI 211 ************.******************************************************** PP TIGR01350 206 lpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnl 271 lp++d evsk++++ l k+g++++ ++kvt + k+ ++ + ve + +e++ea+ vLva+Grkp + lcl|NCBI__GCF_000009985.1:WP_011386317.1 212 LPFNDGEVSKQMQRLLAKQGMEFKLGTKVTGIAKKGKTATvtVEPAAGgAAEKIEADSVLVAIGRKPYT 280 ******************************877776665533666555689****************** PP TIGR01350 272 eelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidyk 340 e+lgl+k+gv ld+rg++++d ++rtnvpgiyaiGDv+g++mLAh+A++egv ae +ag++ +++y+ lcl|NCBI__GCF_000009985.1:WP_011386317.1 281 EGLGLDKVGVALDKRGFVQIDGHFRTNVPGIYAIGDVVGGAMLAHKAEEEGVALAEILAGQHG-HVNYE 348 ************************************************************998.9**** PP TIGR01350 341 avPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahiv 409 a+P+v+yt PevasvG+teeq+k+egi++k+gkfpf+ang+a++++e dGfvkv++ +t+++lGahiv lcl|NCBI__GCF_000009985.1:WP_011386317.1 349 AIPAVVYTWPEVASVGKTEEQLKAEGIAYKAGKFPFTANGRARSMNEVDGFVKVLACATTDKVLGAHIV 417 ********************************************************************* PP TIGR01350 410 gaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaih 460 g++a +li+e++la+e+++ +e++a+t+h+HP l+Ea+kea+la+ g+++h lcl|NCBI__GCF_000009985.1:WP_011386317.1 418 GPNAGDLIAEVVLAMEFGAASEDIARTCHAHPGLGEAVKEACLAVDGRPLH 468 ************************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (469 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 9.16 // [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