Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate AO356_19705 AO356_19705 dihydrolipoamide dehydrogenase
Query= CharProtDB::CH_015561 (478 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_19705 Length = 478 Score = 875 bits (2262), Expect = 0.0 Identities = 450/478 (94%), Positives = 460/478 (96%) Query: 1 MTQKFDVVVIGAGPGGYVAAIKAAQLGLKTACIEKYTDAEGKLALGGTCLNVGCIPSKAL 60 MTQKFDVVVIGAGPGGYVAAIKAAQLGL TACIEKYTD EGK ALGGTCLNVGCIPSKAL Sbjct: 1 MTQKFDVVVIGAGPGGYVAAIKAAQLGLTTACIEKYTDGEGKQALGGTCLNVGCIPSKAL 60 Query: 61 LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTSIQG 120 LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLT GVATLFKANGVTSIQG Sbjct: 61 LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTSGVATLFKANGVTSIQG 120 Query: 121 HGKLLAGKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGALEFQAV 180 HGKLL GKKVEVTK DG+ EVIEAENVILA GSRPIDIPPAPVDQNVIVDSTGALEFQ+V Sbjct: 121 HGKLLLGKKVEVTKPDGSVEVIEAENVILAPGSRPIDIPPAPVDQNVIVDSTGALEFQSV 180 Query: 181 PKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQGLDIK 240 PKRLGVIGAGVIGLELGSVW+RLGA+VTVLEALDTFLMAAD AVSKEA KTLTKQGLDIK Sbjct: 181 PKRLGVIGAGVIGLELGSVWSRLGAQVTVLEALDTFLMAADAAVSKEALKTLTKQGLDIK 240 Query: 241 LGARVTGSKVNGNEVEVTYTNAEGEQKITFDKLIVAVGRRPVTTDLLAADSGVTIDERGY 300 LGARVTGSKVNG EV V YT+A GEQ ITFDKLIVAVGRRPVTTDLLAADSGV +DERG+ Sbjct: 241 LGARVTGSKVNGEEVVVNYTDANGEQTITFDKLIVAVGRRPVTTDLLAADSGVDLDERGF 300 Query: 301 IFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH 360 I VDD+CAT+VPGV+AIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH Sbjct: 301 IKVDDFCATTVPGVFAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH 360 Query: 361 PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI 420 PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI Sbjct: 361 PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI 420 Query: 421 GPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKKR 478 GPSAAELVQQGAI MEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKKR Sbjct: 421 GPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKKR 478 Lambda K H 0.316 0.133 0.374 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: 915 Number of extensions: 17 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: 478 Length of database: 478 Length adjustment: 34 Effective length of query: 444 Effective length of database: 444 Effective search space: 197136 Effective search space used: 197136 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 AO356_19705 AO356_19705 (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.19749.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-163 531.1 11.3 1.3e-163 530.9 11.3 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 AO356_19705 dihydrolipoamide deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 AO356_19705 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 530.9 11.3 1.3e-163 1.3e-163 1 461 [] 4 472 .. 4 472 .. 0.97 Alignments for each domain: == domain 1 score: 530.9 bits; conditional E-value: 1.3e-163 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalve.......keklGGtClnvGCiPtKalLksaev 56 ++dvvviG+GpgGYvaAi+aaqlgl +a++e k+ lGGtClnvGCiP+KalL s+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 4 KFDVVVIGAGPGGYVAAIKAAQLGLTTACIEkytdgegKQALGGTCLNVGCIPSKALLDSSWK 66 59*****************************44444334579********************* PP TIGR01350 57 veelke.akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkke 118 ++e+ke ++ +gi++ +vk+d+++++ rk +vk+l++Gv++L+k n+v++i+G++kll k+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 67 YKEAKEsFNVHGISTGEVKMDVAAMVGRKAGIVKNLTSGVATLFKANGVTSIQGHGKLLLGKK 129 ******9******************************************************** PP TIGR01350 119 vevkkekke.kkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGv 180 vev+k +++ +++ea+n+i+A Gs+p+ +p +d++v+++s++ale+++vp++l ++G+Gv lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 130 VEVTKPDGSvEVIEAENVILAPGSRPIDIPP-APVDQNVIVDSTGALEFQSVPKRLGVIGAGV 191 *****998889*******************9.8999999************************ PP TIGR01350 181 iGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeede 243 iG+E++s++++lG++vtv+e+ld+ l a da vsk++ k+l+k+g++i+ +a+vt + + +e lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 192 IGLELGSVWSRLGAQVTVLEALDTFLMAADAAVSKEALKTLTKQGLDIKLGARVTGSKVNGEE 254 *******************************************************98888888 PP TIGR01350 244 vvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyai 305 vvv+ + ++t++ +k++vavGr+p +++l + gv+lderg+ikvd+ + t+vpg++ai lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 255 VVVNYTDAnGEQTITFDKLIVAVGRRPVTTDLLAADSGVDLDERGFIKVDDFCATTVPGVFAI 317 886666655679*************************************************** PP TIGR01350 306 GDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegie 368 GDv++++mLAh+As+eg++++e+i g+++ +++y+++Psviyt+Pe+a vG+te+ +k+eg+e lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 318 GDVVRGMMLAHKASEEGIMVVERIKGHKA-QMNYDLIPSVIYTHPEIAWVGKTEQALKAEGVE 379 **************************665.9******************************** PP TIGR01350 369 vkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltve 431 v+vg fpfaa+g+a+a+++t Gfvkvi+d kt+++lG+h++g++a+el+++ a+ +e+++++e lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 380 VNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVIGPSAAELVQQGAIGMEFGTSAE 442 *************************************************************** PP TIGR01350 432 elaktihpHPtlsEaikeaalaalgkaihv 461 +l ++++ HPtlsEa++eaala++g aihv lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19705 443 DLGMMVFSHPTLSEALHEAALAVNGGAIHV 472 ****************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (478 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: 7.53 // [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