Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate AO356_22975 AO356_22975 dihydrolipoamide dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_22975 (461 letters) >lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 AO356_22975 dihydrolipoamide dehydrogenase Length = 461 Score = 908 bits (2346), Expect = 0.0 Identities = 461/461 (100%), Positives = 461/461 (100%) Query: 1 MQQTLNTTLLIIGGGPGGYVAAIRAGQLGISTILVEGQALGGTCLNIGCIPSKALIHVAE 60 MQQTLNTTLLIIGGGPGGYVAAIRAGQLGISTILVEGQALGGTCLNIGCIPSKALIHVAE Sbjct: 1 MQQTLNTTLLIIGGGPGGYVAAIRAGQLGISTILVEGQALGGTCLNIGCIPSKALIHVAE 60 Query: 61 QFHQTRHHSQGSALGITVAAPTLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK 120 QFHQTRHHSQGSALGITVAAPTLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK Sbjct: 61 QFHQTRHHSQGSALGITVAAPTLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK 120 Query: 121 VIDGKTVEVGDTRIQCEHLLLATGSKSVNLPMLPLGGPIISSTEALAPTSVPKHLVVVGG 180 VIDGKTVEVGDTRIQCEHLLLATGSKSVNLPMLPLGGPIISSTEALAPTSVPKHLVVVGG Sbjct: 121 VIDGKTVEVGDTRIQCEHLLLATGSKSVNLPMLPLGGPIISSTEALAPTSVPKHLVVVGG 180 Query: 181 GYIGLELGIAYRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFD 240 GYIGLELGIAYRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFD Sbjct: 181 GYIGLELGIAYRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFD 240 Query: 241 AQASTLQVRDPNGDTLNLETDRVLVAVGRKPNTQGWNLAALDLAMNGSAVKIDSRCQTSM 300 AQASTLQVRDPNGDTLNLETDRVLVAVGRKPNTQGWNLAALDLAMNGSAVKIDSRCQTSM Sbjct: 241 AQASTLQVRDPNGDTLNLETDRVLVAVGRKPNTQGWNLAALDLAMNGSAVKIDSRCQTSM 300 Query: 301 RNVWAIGDLSGEPMLAHRAMAQGEMVAELIAGQHREFNPTAIAAVCFTDPELVVVGKTPD 360 RNVWAIGDLSGEPMLAHRAMAQGEMVAELIAGQHREFNPTAIAAVCFTDPELVVVGKTPD Sbjct: 301 RNVWAIGDLSGEPMLAHRAMAQGEMVAELIAGQHREFNPTAIAAVCFTDPELVVVGKTPD 360 Query: 361 EAKAAGLDCLVSSFPFAANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAF 420 EAKAAGLDCLVSSFPFAANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAF Sbjct: 361 EAKAAGLDCLVSSFPFAANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAF 420 Query: 421 GQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHL 461 GQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHL Sbjct: 421 GQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHL 461 Lambda K H 0.318 0.134 0.392 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: 833 Number of extensions: 14 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: 461 Length of database: 461 Length adjustment: 33 Effective length of query: 428 Effective length of database: 428 Effective search space: 183184 Effective search space used: 183184 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 AO356_22975 AO356_22975 (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.30093.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-148 481.5 0.7 1.4e-148 481.3 0.7 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 AO356_22975 dihydrolipoamide deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 AO356_22975 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 481.3 0.7 1.4e-148 1.4e-148 3 460 .. 8 460 .. 6 461 .] 0.98 Alignments for each domain: == domain 1 score: 481.3 bits; conditional E-value: 1.4e-148 TIGR01350 3 dvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke... 62 +++iGgGpgGYvaAira+qlg +++lve + lGGtCln GCiP+Kal++ ae +++ ++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 8 TLLIIGGGPGGYVAAIRAGQLGISTILVEGQALGGTCLNIGCIPSKALIHVAEQFHQTRHhsq 70 578*******************************************************99533 PP TIGR01350 63 akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkek 125 + lgi+v+ +ld+ k +e+k+ +v++l++Gv+aLlkk+kv+vi+G ak+ d k+vev +++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 71 GSALGITVAAPTLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAKVIDGKTVEVGDTR 133 3579*******************************************************9998 PP TIGR01350 126 kekkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasi 188 ++ +++++AtGs+ +lp+ l + +i+s+eal+ ++vp++lv+vGgG+iG+E++ + lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 134 ----IQCEHLLLATGSKSVNLPM-LPLGG-PIISSTEALAPTSVPKHLVVVGGGYIGLELGIA 190 ....89*****************.89888.69******************************* PP TIGR01350 189 faklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk 251 ++klG++v+v+e+++rilpa d e+++ ++++lk+ gvk++ +++v+ +++ +++v+ ++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 191 YRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFDAQASTLQVRDPNG 253 *********************************************************999999 PP TIGR01350 252 evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmL 314 ++ +le+++vLvavGrkpn+++ +l++l++ ++ a+k+d++++t++ +++aiGD+ g++mL lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 254 DTLNLETDRVLVAVGRKPNTQGWNLAALDLAMNG-SAVKIDSRCQTSMRNVWAIGDLSGEPML 315 9********************************9.78************************** PP TIGR01350 315 AhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfa 377 Ah+A+++g ++ae iag+++ e++ +a+ +v +t+Pe+ +vG+t ++ak++g ++ v++fpfa lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 316 AHRAMAQGEMVAELIAGQHR-EFNPTAIAAVCFTDPELVVVGKTPDEAKAAGLDCLVSSFPFA 377 *****************998.9***************************************** PP TIGR01350 378 angkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpH 440 ang+a++le ++Gfv+v++ ++ + i+G + vg +sel + + +e+++++e++a tih+H lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 378 ANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAFGQSLEMGARLEDIAGTIHAH 440 *************************************************************** PP TIGR01350 441 PtlsEaikeaalaalgkaih 460 Ptl+Ea++eaal alg+a+h lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22975 441 PTLGEAVQEAALRALGHALH 460 *****************999 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (461 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: 7.50 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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