Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Pf1N1B4_4477 Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3543 (460 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 Length = 460 Score = 861 bits (2224), Expect = 0.0 Identities = 435/460 (94%), Positives = 450/460 (97%) Query: 1 MQTLNTTLLIIGGGPGGYVTAIRAGQLGIPTILVEGQSLGGTCLNIGCIPSKALIHVAEQ 60 MQTLNTTLLIIGGGPGGYVTAIRAGQLGI TILVEGQSLGGTCLNIGCIPSKALIHVAEQ Sbjct: 1 MQTLNTTLLIIGGGPGGYVTAIRAGQLGISTILVEGQSLGGTCLNIGCIPSKALIHVAEQ 60 Query: 61 FHQTQHHSQHSALGISVSAPTLDIGKSVEWKDGIVDRLTTGVAALLKKNKVQVVQGWAKV 120 FHQTQHHSQHSALGISVSAPTL+IGKSVEWKDGIVDRLTTGV+ALLKK+KVQV+QGWAKV Sbjct: 61 FHQTQHHSQHSALGISVSAPTLNIGKSVEWKDGIVDRLTTGVSALLKKHKVQVIQGWAKV 120 Query: 121 VDGKTVEVGDTRIQCEHLVLATGSKSVNLPMLPIGGPIISSTEALAPTSVPKRLIVVGGG 180 +DGKTVEVGDTRIQCEHLVLATGSKSVNLPMLPIGGPIISSTEALAPTSVPKRLIVVGGG Sbjct: 121 IDGKTVEVGDTRIQCEHLVLATGSKSVNLPMLPIGGPIISSTEALAPTSVPKRLIVVGGG 180 Query: 181 YIGLELGIAYRKLGAEVSVVEAQERILPAYDAELTQPVHDELKKLGVKLYLKHSVQGFDS 240 YIGLELGIAYRKLGAEVSVVEAQ+RILPAYDAELT PVH+ LK+L VKLYLKHSVQGFDS Sbjct: 181 YIGLELGIAYRKLGAEVSVVEAQDRILPAYDAELTHPVHEALKQLDVKLYLKHSVQGFDS 240 Query: 241 SNNTLQVLAPNGETLNLETDQVLVAVGRKPNTQGWNLEALNLDMNGSSIKIDNRCQTSMR 300 NNTLQV+ P+G++LNL+TDQVLVAVGRKPNTQGWNLEALNLDMNGS+IKIDNRCQTSMR Sbjct: 241 VNNTLQVIDPSGDSLNLKTDQVLVAVGRKPNTQGWNLEALNLDMNGSAIKIDNRCQTSMR 300 Query: 301 NVYAIGDLSGEPMLAHRAMAQGEMVAELISGKTREFNPTAIAAVCFTDPELVVVGKTPDE 360 NVYAIGDLSGEPMLAHRAMAQGEMVAELISGK REFNPTAIAAVCFTDPELVVVGKTPDE Sbjct: 301 NVYAIGDLSGEPMLAHRAMAQGEMVAELISGKHREFNPTAIAAVCFTDPELVVVGKTPDE 360 Query: 361 AKAAGWDCIVSSFPFAANGRAMTLESKSGFVRVVARRDNHVIVGWQAVGVGVSELSTAFA 420 AKAAG DCIVSSFPFAANGRAMTLES+SGFVRVVARRDNHVIVGWQAVGVGVSELSTAF Sbjct: 361 AKAAGLDCIVSSFPFAANGRAMTLESRSGFVRVVARRDNHVIVGWQAVGVGVSELSTAFG 420 Query: 421 QSLEMGARLEDIGGTIHAHPTLGEAVQEAALRALGHALHL 460 QSLEMGARLEDI GTIHAHPTLGEAVQEAALRALGHALHL Sbjct: 421 QSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHL 460 Lambda K H 0.317 0.134 0.388 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: 765 Number of extensions: 16 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: 460 Length of database: 460 Length adjustment: 33 Effective length of query: 427 Effective length of database: 427 Effective search space: 182329 Effective search space used: 182329 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 (21.6 bits) S2: 51 (24.3 bits)
Align candidate Pf1N1B4_4477 (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.18556.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-149 483.5 1.6 3.5e-149 483.3 1.6 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 Dihydrolipoamide dehydrogenase o Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehyd # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 483.3 1.6 3.5e-149 3.5e-149 3 460 .. 7 459 .. 5 460 .] 0.97 Alignments for each domain: == domain 1 score: 483.3 bits; conditional E-value: 3.5e-149 TIGR01350 3 dvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke...a 63 +++iGgGpgGYv+Aira+qlg +++lve ++lGGtCln GCiP+Kal++ ae +++ ++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 7 TLLIIGGGPGGYVTAIRAGQLGISTILVEGQSLGGTCLNIGCIPSKALIHVAEQFHQTQHhsqH 70 578******************************************************9995434 PP TIGR01350 64 kelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke 127 + lgi+v+ +l++ k +e+k+ +v++l++Gv+aLlkk+kv+vi+G ak+ d k+vev +++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 71 SALGISVSAPTLNIGKSVEWKDGIVDRLTTGVSALLKKHKVQVIQGWAKVIDGKTVEVGDTR-- 132 568*******************************************************9998.. PP TIGR01350 128 kkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifak 191 ++ +++++AtGs+ +lp+ l + +i+s+eal+ ++vp++l++vGgG+iG+E++ +++k lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 133 --IQCEHLVLATGSKSVNLPM-LPIGG-PIISSTEALAPTSVPKRLIVVGGGYIGLELGIAYRK 192 ..89*****************.99998.69********************************** PP TIGR01350 192 lGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkkevet 255 lG++v+v+e++drilpa dae+++ ++++lk+ vk++ +++v+ + +++++v +++ + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 193 LGAEVSVVEAQDRILPAYDAELTHPVHEALKQLDVKLYLKHSVQGFDSVNNTLQVIDPSGDSLN 256 *****************************************************987777789** PP TIGR01350 256 leaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAs 319 l++++vLvavGrkpn+++ +le+l+++++ aik+d++++t++ ++yaiGD+ g++mLAh+A+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 257 LKTDQVLVAVGRKPNTQGWNLEALNLDMNG-SAIKIDNRCQTSMRNVYAIGDLSGEPMLAHRAM 319 *****************************9.78******************************* PP TIGR01350 320 kegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkal 383 ++g ++ae i gk++ e++ +a+ +v +t+Pe+ +vG+t ++ak++g ++ v++fpfaang+a+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 320 AQGEMVAELISGKHR-EFNPTAIAAVCFTDPELVVVGKTPDEAKAAGLDCIVSSFPFAANGRAM 382 ************998.9*********************************************** PP TIGR01350 384 aleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEai 447 +le ++Gfv+v++ ++ + i+G + vg +sel + + +e+++++e++a tih+HPtl+Ea+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 383 TLESRSGFVRVVARRDNHVIVGWQAVGVGVSELSTAFGQSLEMGARLEDIAGTIHAHPTLGEAV 446 **************************************************************** PP TIGR01350 448 keaalaalgkaih 460 +eaal alg+a+h lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477 447 QEAALRALGHALH 459 **********999 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (460 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 8.19 // [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