Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Pf6N2E2_478 Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)
Query= reanno::pseudo6_N2E2:Pf6N2E2_478 (461 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 Length = 461 Score = 909 bits (2349), Expect = 0.0 Identities = 461/461 (100%), Positives = 461/461 (100%) Query: 1 MQQTLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAE 60 MQQTLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAE Sbjct: 1 MQQTLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAE 60 Query: 61 QFHQTRHHSQGSALGITVSAPSLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK 120 QFHQTRHHSQGSALGITVSAPSLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK Sbjct: 61 QFHQTRHHSQGSALGITVSAPSLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK 120 Query: 121 VIDGKTVEVGDTRIQCEHLLLATGSKSVDLPMLPVGGPIISSTEALAPTSVPKHLVVVGG 180 VIDGKTVEVGDTRIQCEHLLLATGSKSVDLPMLPVGGPIISSTEALAPTSVPKHLVVVGG Sbjct: 121 VIDGKTVEVGDTRIQCEHLLLATGSKSVDLPMLPVGGPIISSTEALAPTSVPKHLVVVGG 180 Query: 181 GYIGLELGIAYRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFD 240 GYIGLELGIAYRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFD Sbjct: 181 GYIGLELGIAYRKLGAEVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFD 240 Query: 241 AQASTLQVRDPAGDTLNLDTDRVLVAVGRKPNTQGWNLEALNLAMNGAAVKIDQRCQTSM 300 AQASTLQVRDPAGDTLNLDTDRVLVAVGRKPNTQGWNLEALNLAMNGAAVKIDQRCQTSM Sbjct: 241 AQASTLQVRDPAGDTLNLDTDRVLVAVGRKPNTQGWNLEALNLAMNGAAVKIDQRCQTSM 300 Query: 301 RNVWAIGDLSGEPMLAHRAMAQGEMVAELIAGQHREFNPTAIAAVCFTDPELVVVGKTPD 360 RNVWAIGDLSGEPMLAHRAMAQGEMVAELIAGQHREFNPTAIAAVCFTDPELVVVGKTPD Sbjct: 301 RNVWAIGDLSGEPMLAHRAMAQGEMVAELIAGQHREFNPTAIAAVCFTDPELVVVGKTPD 360 Query: 361 EAKAAGLDCIVSSFPFAANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAF 420 EAKAAGLDCIVSSFPFAANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAF Sbjct: 361 EAKAAGLDCIVSSFPFAANGRAMTLESKSGFVRVVARRDNHLIVGWQAVGVGVSELSTAF 420 Query: 421 GQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHL 461 GQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHL Sbjct: 421 GQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHL 461 Lambda K H 0.318 0.135 0.394 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: 836 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 Pf6N2E2_478 (Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4))
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.1510.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-148 481.1 0.8 1.9e-148 480.9 0.8 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 Dihydrolipoamide dehydrogenase o Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydr # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 480.9 0.8 1.9e-148 1.9e-148 3 460 .. 8 460 .. 6 461 .] 0.98 Alignments for each domain: == domain 1 score: 480.9 bits; conditional E-value: 1.9e-148 TIGR01350 3 dvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke...ak 64 +++iGgGpgGYvaAira+qlg ++lve + lGGtCln GCiP+Kal++ ae +++ ++ + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 8 TLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAEQFHQTRHhsqGS 72 578*******************************************************9953335 PP TIGR01350 65 elgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekk 129 lgi+v+ +ld+ k +e+k+ +v++l++Gv+aLlkk+kv+vi+G ak+ d k+vev +++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 73 ALGITVSAPSLDIGKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAKVIDGKTVEVGDTR---- 133 79*******************************************************9998.... PP TIGR01350 130 leakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGv 194 ++ +++++AtGs+ lp+ l + + +i+s+eal+ ++vp++lv+vGgG+iG+E++ +++klG+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 134 IQCEHLLLATGSKSVDLPM-LPVGG-PIISSTEALAPTSVPKHLVVVGGGYIGLELGIAYRKLGA 196 89*****************.99998.69************************************* PP TIGR01350 195 kvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkkevetleae 259 +v+v+e+++rilpa d e+++ ++++lk+ gvk++ +++v+ +++ +++v+ +++ +l+++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 197 EVSVVEAQERILPAYDGELTQPVHEALKQLGVKLYLKHSVEGFDAQASTLQVRDPAGDTLNLDTD 261 ***************************************************99999999****** PP TIGR01350 260 kvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvv 324 +vLvavGrkpn+++ +le+l++ ++ a+k+d++++t++ +++aiGD+ g++mLAh+A+++g + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 262 RVLVAVGRKPNTQGWNLEALNLAMNG-AAVKIDQRCQTSMRNVWAIGDLSGEPMLAHRAMAQGEM 325 *************************9.78************************************ PP TIGR01350 325 aaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetd 389 +ae iag+++ e++ +a+ +v +t+Pe+ +vG+t ++ak++g ++ v++fpfaang+a++le ++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 326 VAELIAGQHR-EFNPTAIAAVCFTDPELVVVGKTPDEAKAAGLDCIVSSFPFAANGRAMTLESKS 389 *******998.9***************************************************** PP TIGR01350 390 GfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaa 454 Gfv+v++ ++ + i+G + vg +sel + + +e+++++e++a tih+HPtl+Ea++eaal a lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 390 GFVRVVARRDNHLIVGWQAVGVGVSELSTAFGQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRA 454 ***************************************************************** PP TIGR01350 455 lgkaih 460 lg+a+h lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_478 455 LGHALH 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.92 // [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