Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_003941477.1 C1M55_RS07790 dihydrolipoyl dehydrogenase
Query= BRENDA::P9WHH8 (464 letters) >NCBI__GCF_002893965.1:WP_003941477.1 Length = 467 Score = 731 bits (1887), Expect = 0.0 Identities = 361/465 (77%), Positives = 409/465 (87%), Gaps = 2/465 (0%) Query: 2 THYDVVVLGAGPGGYVAAIRAAQLGLSTAIVEPKYWGGVCLNVGCIPSKALLRNAELVHI 61 +HYDVVVLGAGPGGYVAAIRAAQLGLSTAI+E KYWGGVCLNVGCIPSKALLRNAEL HI Sbjct: 3 SHYDVVVLGAGPGGYVAAIRAAQLGLSTAIIEQKYWGGVCLNVGCIPSKALLRNAELAHI 62 Query: 62 FTKDAKAFGISGEVTFDYGIAYDRSRKVAEGRVAGVHFLMKKNKITEIHGYGTFADANTL 121 FTK+AK FG+SG+V+FD+G A+DRSRKVA+GRV G+HFLMKKNKI E G GTF DANT+ Sbjct: 63 FTKEAKTFGMSGDVSFDFGSAFDRSRKVADGRVKGIHFLMKKNKIPEYDGKGTFVDANTI 122 Query: 122 LVDLNDGGTESVTFDNAIIATGSSTRLVPGTSLSANVVTYEEQILSRELPKSIIIAGAGA 181 V+L+ GGTE++TFDNAIIATGS T+L+PGTSLS NVVTYEEQIL+R+LP SI+I GAGA Sbjct: 123 SVELSKGGTETITFDNAIIATGSYTKLLPGTSLSENVVTYEEQILTRDLPGSILIVGAGA 182 Query: 182 IGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSKEIEKQFKKLGVTILTATKVESIADG 241 IGMEFGYVLKNYGVDVTIVEFL RALPNEDADVSKEI KQ+KKLGVTI T V+SI+D Sbjct: 183 IGMEFGYVLKNYGVDVTIVEFLDRALPNEDADVSKEIAKQYKKLGVTIKTGAAVQSISDD 242 Query: 242 GSQVTVTV--TKDGVAQELKAEKVLQAIGFAPNVEGYGLDKAGVALTDRKAIGVDDYMRT 299 GS+VTV++ K G + + +KVLQ++GFAP VEG+GL+ GVALTDR AI +DDYMRT Sbjct: 243 GSKVTVSIKDNKSGEIETVVVDKVLQSVGFAPRVEGFGLENTGVALTDRGAIAIDDYMRT 302 Query: 300 NVGHIYAIGDVNGLLQLAHVAEAQGVVAAETIAGAETLTLGDHRMLPRATFCQPNVASFG 359 NV HI+AIGDV LQLAHVAEAQ VVAAETI GAET TLGD+RM+PRATFCQP VASFG Sbjct: 303 NVPHIFAIGDVTAKLQLAHVAEAQAVVAAETIGGAETQTLGDYRMMPRATFCQPQVASFG 362 Query: 360 LTEQQARNEGYDVVVAKFPFTANAKAHGVGDPSGFVKLVADAKHGELLGGHLVGHDVAEL 419 LTE+QA+ EGYDV VA FPF AN KAHG+GDP+GFVKL+AD K+GELLGGHL+G DV+EL Sbjct: 363 LTEEQAKAEGYDVKVANFPFAANGKAHGLGDPTGFVKLIADKKYGELLGGHLIGPDVSEL 422 Query: 420 LPELTLAQRWDLTASELARNVHTHPTMSEALQECFHGLVGHMINF 464 LPELTLAQ+WDLT +ELARNVHTHPT+SEALQE HGL GHMINF Sbjct: 423 LPELTLAQKWDLTVNELARNVHTHPTLSEALQEAIHGLAGHMINF 467 Lambda K H 0.318 0.136 0.390 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: 745 Number of extensions: 19 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: 464 Length of database: 467 Length adjustment: 33 Effective length of query: 431 Effective length of database: 434 Effective search space: 187054 Effective search space used: 187054 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: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_003941477.1 C1M55_RS07790 (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.1994233.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-171 557.0 1.3 1.8e-171 556.8 1.3 1.0 1 NCBI__GCF_002893965.1:WP_003941477.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002893965.1:WP_003941477.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 556.8 1.3 1.8e-171 1.8e-171 1 460 [. 4 466 .. 4 467 .] 0.97 Alignments for each domain: == domain 1 score: 556.8 bits; conditional E-value: 1.8e-171 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke.akelgieven 72 +ydvvv+G+GpgGYvaAiraaqlgl++a++e++++GG+ClnvGCiP+KalL++ae+++ +++ ak++g+ + + NCBI__GCF_002893965.1:WP_003941477.1 4 HYDVVVLGAGPGGYVAAIRAAQLGLSTAIIEQKYWGGVCLNVGCIPSKALLRNAELAHIFTKeAKTFGM-SGD 75 69********************************************************99988*****9.668 PP TIGR01350 73 vkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGsepr 144 v++d+ ++ +r++kv + v+G+++L+kknk+ ++ G+++++d+++++v+ +k+ ++++++n+iiAtGs + NCBI__GCF_002893965.1:WP_003941477.1 76 VSFDFGSAFDRSRKVADGRVKGIHFLMKKNKIPEYDGKGTFVDANTISVELSKGGtETITFDNAIIATGSYTK 148 **************************************************9887669**************** PP TIGR01350 145 elplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvl 217 lp+ + +e v+t+ee++ + +p s++ivG+G+iG+Ef+++++++Gv+vt++e+ldr lp++da+vsk++ NCBI__GCF_002893965.1:WP_003941477.1 149 LLPG-TSLSE-NVVTYEEQILTRDLPGSILIVGAGAIGMEFGYVLKNYGVDVTIVEFLDRALPNEDADVSKEI 219 ****.66665.5999999999**************************************************** PP TIGR01350 218 kkklkkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnleelgleklgvelderg 287 +k++kk gv+i+t+a v++++++ +v+ ++ +k+ e+et+ ++kvL +vG+ p++e++gle++gv l++rg NCBI__GCF_002893965.1:WP_003941477.1 220 AKQYKKLGVTIKTGAAVQSISDDGSKVTvsIKDNKSgEIETVVVDKVLQSVGFAPRVEGFGLENTGVALTDRG 292 ***************************955555555799********************************** PP TIGR01350 288 aikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks.eidykavPsviytePevasvGlte 359 ai +d+++rtnvp+i+aiGDv++kl+LAhvA++++vvaae+i g+e++ dy+++P++++++P+vas+Glte NCBI__GCF_002893965.1:WP_003941477.1 293 AIAIDDYMRTNVPHIFAIGDVTAKLQLAHVAEAQAVVAAETIGGAETQtLGDYRMMPRATFCQPQVASFGLTE 365 ********************************************9988788********************** PP TIGR01350 360 eqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltvee 432 eqak+eg++vkv++fpfaangka l++ +Gfvk+i+dkk+ge+lG h++g+++sel+ el+la +++ltv+e NCBI__GCF_002893965.1:WP_003941477.1 366 EQAKAEGYDVKVANFPFAANGKAHGLGDPTGFVKLIADKKYGELLGGHLIGPDVSELLPELTLAQKWDLTVNE 438 ************************************************************************* PP TIGR01350 433 laktihpHPtlsEaikeaalaalgkaih 460 la+ +h+HPtlsEa++ea++ + g++i+ NCBI__GCF_002893965.1:WP_003941477.1 439 LARNVHTHPTLSEALQEAIHGLAGHMIN 466 ***********************99997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (467 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 28.82 // [ok]
This GapMind analysis is from Sep 24 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