Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate WP_036136112.1 N800_RS06360 dihydrolipoyl dehydrogenase
Query= SwissProt::P14218 (478 letters) >NCBI__GCF_000768355.1:WP_036136112.1 Length = 480 Score = 536 bits (1381), Expect = e-157 Identities = 284/476 (59%), Positives = 348/476 (73%), Gaps = 4/476 (0%) Query: 3 QKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKALLD 62 Q FDVVVIG GP GY AAIRAAQLGLKTACI+ +GK+GK ALGGTCL VGCIPSKALLD Sbjct: 5 QNFDVVVIGGGPAGYHAAIRAAQLGLKTACIDAALGKDGKPALGGTCLRVGCIPSKALLD 64 Query: 63 SSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEGHG 122 SS ++ F HGI + IDV MVARK IVK TGGIA+LFKAN V +F G G Sbjct: 65 SSRQFWNMGHIFDQHGISFEKPAIDVKKMVARKDGIVKQFTGGIASLFKANKVAAFYGFG 124 Query: 123 KLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQAVPK 182 +L V+VT DG L+ NVIIA+GS +E+P A + IVD+ G L+F+AVP+ Sbjct: 125 QLQPGNVVKVTQHDGSVVELKGTNVIIAAGSDSIELPFAKFDGECIVDNVGGLDFEAVPE 184 Query: 183 KLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLNIRLG 242 +LGVIGAGVIGLELGSVW RLGA+VT+LEAL FL AAD ++ K + + KQGL+I+LG Sbjct: 185 RLGVIGAGVIGLELGSVWNRLGAKVTILEALPGFLSAADAEVGKVSAREFKKQGLDIKLG 244 Query: 243 ARVTASEV----KKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGVTLDER 298 A+V+ +EV KKK+V +T+TDA GEQ DKL+VAVGRR T LLA +GV ++ER Sbjct: 245 AKVSKAEVKGKGKKKEVELTYTDAAGEQTLVVDKLLVAVGRRAATKGLLAEGTGVRVNER 304 Query: 299 GFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVIY 358 G I VD+HC T V GV+A+GD VRG MLAHK EEG+ VAE IAG +N+D IP VIY Sbjct: 305 GQIEVDEHCHTGVDGVWAVGDCVRGPMLAHKGFEEGIAVAELIAGLPGHVNFDTIPWVIY 364 Query: 359 THPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGVH 418 T PEIAWVGKTE+ LKAEGV G+FPFAA GRA+A + G VKVIA A+TDRVLG+H Sbjct: 365 TEPEIAWVGKTEEQLKAEGVPYKAGSFPFAAVGRAVAMAEPAGFVKVIAHAETDRVLGMH 424 Query: 419 VIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIHIAN 474 ++G + +ELV +G + MEF SA+DL + +HP+LSEA+H+AA+AV+ AIH AN Sbjct: 425 LVGANVSELVHEGVLTMEFSGSADDLARICHAHPSLSEAVHDAAMAVHKRAIHKAN 480 Lambda K H 0.316 0.134 0.375 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: 712 Number of extensions: 28 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: 480 Length adjustment: 34 Effective length of query: 444 Effective length of database: 446 Effective search space: 198024 Effective search space used: 198024 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 WP_036136112.1 N800_RS06360 (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.2834393.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-153 497.1 4.0 2.6e-153 496.9 4.0 1.0 1 NCBI__GCF_000768355.1:WP_036136112.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000768355.1:WP_036136112.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 496.9 4.0 2.6e-153 2.6e-153 1 460 [. 6 477 .. 6 478 .. 0.95 Alignments for each domain: == domain 1 score: 496.9 bits; conditional E-value: 2.6e-153 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalve.......keklGGtClnvGCiPtKalLksaevveelke.ake 65 ++dvvviGgGp+GY aAiraaqlglk+a+++ k lGGtCl vGCiP+KalL s+ + ++ + +++ NCBI__GCF_000768355.1:WP_036136112.1 6 NFDVVVIGGGPAGYHAAIRAAQLGLKTACIDaalgkdgKPALGGTCLRVGCIPSKALLDSSRQFWNMGHiFDQ 78 69****************************85555444568******************************** PP TIGR01350 66 lgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniii 137 +gi+ e+ ++d++k+++rk+ +vk+ +gG++ L+k nkv + G ++l+ + v+v++++++ +l+ n+ii NCBI__GCF_000768355.1:WP_036136112.1 79 HGISFEKPAIDVKKMVARKDGIVKQFTGGIASLFKANKVAAFYGFGQLQPGNVVKVTQHDGSvVELKGTNVII 151 ***********************************************************9887788899**** PP TIGR01350 138 AtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpald 210 A Gs+ +elp+ ++d+++++++ + l ++ vpe+l ++G+GviG+E++s++++lG+kvt++e+l+ l a d NCBI__GCF_000768355.1:WP_036136112.1 152 AAGSDSIELPF-AKFDGECIVDNVGGLDFEAVPERLGVIGAGVIGLELGSVWNRLGAKVTILEALPGFLSAAD 223 ***********.99*********************************************************** PP TIGR01350 211 aevskvlkkklkkkgvkiltnakvt..eve..keedevvveakkk.evetleaekvLvavGrkpnleelglek 278 aev kv ++++kk+g++i+ +akv+ ev+ +++ev+++ + ++tl ++k+LvavGr++ +++l e NCBI__GCF_000768355.1:WP_036136112.1 224 AEVGKVSAREFKKQGLDIKLGAKVSkaEVKgkGKKKEVELTYTDAaGEQTLVVDKLLVAVGRRAATKGLLAEG 296 ************************9553331134455554444444679************************ PP TIGR01350 279 lgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePe 351 +gv+++erg+i+vde+++t v+g++a+GD+++++mLAh+ ++eg+ +ae iag +++ +++P viytePe NCBI__GCF_000768355.1:WP_036136112.1 297 TGVRVNERGQIEVDEHCHTGVDGVWAVGDCVRGPMLAHKGFEEGIAVAELIAGLPG-HVNFDTIPWVIYTEPE 368 *****************************************************777.9*************** PP TIGR01350 352 vasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalav 424 +a vG+teeq+k+eg+ +k+g+fpfaa+g+a+a+ e Gfvkvi++ +t+++lG+h+vga++sel++e +l + NCBI__GCF_000768355.1:WP_036136112.1 369 IAWVGKTEEQLKAEGVPYKAGSFPFAAVGRAVAMAEPAGFVKVIAHAETDRVLGMHLVGANVSELVHEGVLTM 441 ************************************************************************* PP TIGR01350 425 eleltveelaktihpHPtlsEaikeaalaalgkaih 460 e+ +++++la+++h+HP+lsEa+++aa a+ ++aih NCBI__GCF_000768355.1:WP_036136112.1 442 EFSGSADDLARICHAHPSLSEAVHDAAMAVHKRAIH 477 **********************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (480 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: 00:00:00.01 # Mc/sec: 15.21 // [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