Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_017367571.1 BA79_RS11110 dihydrolipoyl dehydrogenase
Query= BRENDA::P50970 (466 letters) >NCBI__GCF_000691145.1:WP_017367571.1 Length = 474 Score = 380 bits (977), Expect = e-110 Identities = 206/475 (43%), Positives = 300/475 (63%), Gaps = 10/475 (2%) Query: 1 MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60 MA +DL++LGGG GGYVAAIRA+QL LK A+VE+ LGG CL+ GCIP+K+LLRSAEVY Sbjct: 1 MATEYDLVILGGGTGGYVAAIRASQLGLKTAVVEKSKLGGTCLHKGCIPSKALLRSAEVY 60 Query: 61 HEMQNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQ 120 ++ A +G+ + + R E+ +LA GVK L+++ K++V G+G++ G Sbjct: 61 QTVKRAADFGVEASGIALQFASVQKRKTEIVDKLAGGVKHLMKQGKIDVYEGIGRILGPS 120 Query: 121 -------QMLVETTEGEE-KILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAM 172 + VE G+E ++L K +IIATG+R R LP + +DG HI T AL+ + Sbjct: 121 IFSPMPGTISVEMANGDENEMLIPKQVIIATGSRPRVLPGLEADGTHILTSDEALELQEL 180 Query: 173 PKKLLVIGSGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRIL 232 P+ +L++G G IGIE+AS DFG +V+++E A +ILP ED ++S + K K+GI ++ Sbjct: 181 PQSMLIVGGGVIGIEWASMLNDFGVKVTVIEFADRILPTEDQDISKEMEKLLTKKGITLV 240 Query: 233 TQSALQNLTPDDEGVTAEIAGADGKVTKE-RFSHAIVAIGVVANVENIGLDKLGIKLDRG 291 T + + T + +I G T+ ++++G V NVE IGL+ I+ + Sbjct: 241 TNAKVLPDTAEKHENLVKIQVEQGGDTQSFEAEKLLLSVGRVPNVEGIGLENTDIQTENH 300 Query: 292 FIAVDGFGRTNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCT 351 I V+ +T H++AIGDV G LAH ASH+G+IA E +AG D PL+ + C Sbjct: 301 GIVVNEHYQTKESHIYAIGDVIGGLQLAHVASHEGMIAVEHMAGQDP-KPLDETLVSKCV 359 Query: 352 YARPQVASVGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGA 411 Y+ P+ ASVGLTE+ A++QGY VKIG FPF+A GKA+ G +DGFVK + D + +LG Sbjct: 360 YSHPETASVGLTEQAAKEQGYEVKIGKFPFMAIGKALVFGESDGFVKIIADQKTDDILGI 419 Query: 412 HMVGAEVTEMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALHF 466 HM+G VT+MI +A+ L+ T E+ +TI PHPTLSEA+ E+ LA G+A+HF Sbjct: 420 HMIGPHVTDMISEAGLAKVLDATPWEVGQTIHPHPTLSEAIGEAALAVDGKAIHF 474 Lambda K H 0.319 0.135 0.393 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: 594 Number of extensions: 28 Number of successful extensions: 4 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: 466 Length of database: 474 Length adjustment: 33 Effective length of query: 433 Effective length of database: 441 Effective search space: 190953 Effective search space used: 190953 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_017367571.1 BA79_RS11110 (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.1609082.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-183 597.0 9.2 1.3e-183 596.8 9.2 1.0 1 NCBI__GCF_000691145.1:WP_017367571.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000691145.1:WP_017367571.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 596.8 9.2 1.3e-183 1.3e-183 1 461 [] 4 474 .] 4 474 .] 0.98 Alignments for each domain: == domain 1 score: 596.8 bits; conditional E-value: 1.3e-183 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenv 73 eyd+v++GgG+gGYvaAira+qlglk+a+vek+klGGtCl++GCiP+KalL+saev++++k a+++g+e++++ NCBI__GCF_000691145.1:WP_017367571.1 4 EYDLVILGGGTGGYVAAIRASQLGLKTAVVEKSKLGGTCLHKGCIPSKALLRSAEVYQTVKRAADFGVEASGI 76 69*********************************************************************** PP TIGR01350 74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklld.......kkevevkkekke..kkleakniii 137 +l+++++++rk+++v+kl+gGvk+L+k+ k++v++G +++l+ +++++v++ ++ ++l k++ii NCBI__GCF_000691145.1:WP_017367571.1 77 ALQFASVQKRKTEIVDKLAGGVKHLMKQGKIDVYEGIGRILGpsifspmPGTISVEMANGDenEMLIPKQVII 149 *****************************************99999999899999988877679999****** PP TIGR01350 138 AtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpald 210 AtGs+pr lp+ le+d++ ++ts+ealel+e+p+s++ivGgGviG+E+as+++++Gvkvtvie++drilp++d NCBI__GCF_000691145.1:WP_017367571.1 150 ATGSRPRVLPG-LEADGTHILTSDEALELQELPQSMLIVGGGVIGIEWASMLNDFGVKVTVIEFADRILPTED 221 ***********.************************************************************* PP TIGR01350 211 aevskvlkkklkkkgvkiltnakvt..evekeedevvveakkk.evetleaekvLvavGrkpnleelgleklg 280 +++sk+++k l+kkg++++tnakv + ek+e+ v+++ +++ ++++ eaek+L++vGr pn+e++gle+++ NCBI__GCF_000691145.1:WP_017367571.1 222 QDISKEMEKLLTKKGITLVTNAKVLpdTAEKHENLVKIQVEQGgDTQSFEAEKLLLSVGRVPNVEGIGLENTD 294 ************************997888888889999988889**************************** PP TIGR01350 281 veldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePeva 353 ++++++g i+v+e+++t+ ++iyaiGDvig+l+LAhvAs+eg++a+e++ag+ ++ +d+++v +++y++Pe a NCBI__GCF_000691145.1:WP_017367571.1 295 IQTENHG-IVVNEHYQTKESHIYAIGDVIGGLQLAHVASHEGMIAVEHMAGQDPKPLDETLVSKCVYSHPETA 366 **99977.***************************************************************** PP TIGR01350 354 svGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalavel 426 svGlte+ ake+g+evk+gkfpf+a+gkal+ +e+dGfvk+i+d+kt++ilG+h++g++++++ise+ la l NCBI__GCF_000691145.1:WP_017367571.1 367 SVGLTEQAAKEQGYEVKIGKFPFMAIGKALVFGESDGFVKIIADQKTDDILGIHMIGPHVTDMISEAGLAKVL 439 ************************************************************************* PP TIGR01350 427 eltveelaktihpHPtlsEaikeaalaalgkaihv 461 ++t +e+ +tihpHPtlsEai eaala+ gkaih+ NCBI__GCF_000691145.1:WP_017367571.1 440 DATPWEVGQTIHPHPTLSEAIGEAALAVDGKAIHF 474 *********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (474 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 16.85 // [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