Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate WP_057509361.1 ABB28_RS14820 dihydrolipoyl dehydrogenase
Query= SwissProt::P14218 (478 letters) >NCBI__GCF_001431535.1:WP_057509361.1 Length = 478 Score = 541 bits (1394), Expect = e-158 Identities = 284/478 (59%), Positives = 349/478 (73%), Gaps = 4/478 (0%) Query: 1 MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKAL 60 M+++FDVVVIGAGP GY AAIRAAQLGLKTACI+ +GK+GK ALGGTCL VGCIPSKAL Sbjct: 1 MAEQFDVVVIGAGPAGYHAAIRAAQLGLKTACIDAALGKDGKPALGGTCLRVGCIPSKAL 60 Query: 61 LDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEG 120 LDSS +Y F HGI K IDV AMV RK IVK TGGIA LFKAN V ++ G Sbjct: 61 LDSSRQYWNMGHIFGDHGISFKDARIDVEAMVGRKDKIVKQFTGGIAMLFKANKVAAYYG 120 Query: 121 HGKLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQAV 180 G+L + V+VT DG L+ NVIIA+GS +E+P A + IVD+ G L+F V Sbjct: 121 FGELQKDNVVKVTQHDGSIVELKGTNVIIAAGSDSIELPFAKFDGETIVDNVGGLDFTEV 180 Query: 181 PKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLNIR 240 PK+L VIGAGVIGLELGSVW RLGAEVT+LEAL FL AAD ++ K ALK KQGL+I+ Sbjct: 181 PKRLAVIGAGVIGLELGSVWKRLGAEVTILEALPDFLAAADAEVGKVALKEFKKQGLDIK 240 Query: 241 LGARVTASEV----KKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGVTLD 296 LGA+V+ +EV KK +V +T+TDA GE+ DKL+VAVGRR T LLA +GV ++ Sbjct: 241 LGAKVSKAEVSGKGKKAEVALTYTDAEGEKSLVVDKLLVAVGRRAATKGLLAEGTGVKIN 300 Query: 297 ERGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSV 356 ERG I VD HC T V GV+A+GD VRG MLAHK EEG+ VAE IAG +N+D IP V Sbjct: 301 ERGQIEVDAHCHTGVDGVWAVGDCVRGPMLAHKGFEEGIAVAELIAGEPGHVNFDTIPWV 360 Query: 357 IYTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLG 416 IYT PE+AWVGKTEQ LKAEG+ G+FPFAA+GRA+A + TG VKV+A A+TDR+LG Sbjct: 361 IYTEPELAWVGKTEQQLKAEGIPYKAGSFPFAANGRAVAMIEPTGFVKVLAHAETDRILG 420 Query: 417 VHVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIHIAN 474 +H++G + +ELV +G + MEF SA+DL + +HP+LSE +H+AA+AV+ AIH AN Sbjct: 421 MHLVGANVSELVHEGVLTMEFSGSADDLARICHAHPSLSEVVHDAAMAVSKRAIHKAN 478 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: 685 Number of extensions: 23 Number of successful extensions: 3 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 WP_057509361.1 ABB28_RS14820 (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.23224.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-155 503.5 5.1 3e-155 503.3 5.1 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057509361.1 ABB28_RS14820 dihydrolipoyl dehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057509361.1 ABB28_RS14820 dihydrolipoyl dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 503.3 5.1 3e-155 3e-155 1 460 [. 4 475 .. 4 476 .. 0.95 Alignments for each domain: == domain 1 score: 503.3 bits; conditional E-value: 3e-155 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalve.......keklGGtClnvGCiPtKalLksaevveelke 62 ++dvvviG+Gp+GY aAiraaqlglk+a+++ k lGGtCl vGCiP+KalL s+ + ++ + lcl|NCBI__GCF_001431535.1:WP_057509361.1 4 QFDVVVIGAGPAGYHAAIRAAQLGLKTACIDaalgkdgKPALGGTCLRVGCIPSKALLDSSRQYWNMGH 72 59****************************85555444568**************************** PP TIGR01350 63 .akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kk 129 + ++gi+ ++ ++d+e+++ rk+k+vk+ +gG+++L+k nkv + G ++l++++ v+v++++++ + lcl|NCBI__GCF_001431535.1:WP_057509361.1 73 iFGDHGISFKDARIDVEAMVGRKDKIVKQFTGGIAMLFKANKVAAYYGFGELQKDNVVKVTQHDGSiVE 141 ***************************************************************998888 PP TIGR01350 130 leakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtv 198 l+ n+iiA Gs+ +elp+ ++d+++++++ + l ++evp++l+++G+GviG+E++s++++lG++vt+ lcl|NCBI__GCF_001431535.1:WP_057509361.1 142 LKGTNVIIAAGSDSIELPF-AKFDGETIVDNVGGLDFTEVPKRLAVIGAGVIGLELGSVWKRLGAEVTI 209 9999***************.999999******************************************* PP TIGR01350 199 ielldrilpaldaevskvlkkklkkkgvkiltnakvt..evekeedevv....veakkk.evetleaek 260 +e+l+ l+a daev kv+ k++kk+g++i+ +akv+ ev+ + ++ + + + +++l ++k lcl|NCBI__GCF_001431535.1:WP_057509361.1 210 LEALPDFLAAADAEVGKVALKEFKKQGLDIKLGAKVSkaEVSGKGKKAEvaltY--TDAeGEKSLVVDK 276 *************************************55454444444444423..33335699***** PP TIGR01350 261 vLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaeki 329 +LvavGr++ +++l e +gv+++erg+i+vd++++t v+g++a+GD+++++mLAh+ ++eg+ +ae i lcl|NCBI__GCF_001431535.1:WP_057509361.1 277 LLVAVGRRAATKGLLAEGTGVKINERGQIEVDAHCHTGVDGVWAVGDCVRGPMLAHKGFEEGIAVAELI 345 ********************************************************************* PP TIGR01350 330 agkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdk 398 ag+ +++ +++P viytePe+a vG+te+q+k+egi +k+g+fpfaang+a+a+ e +Gfvkv+++ lcl|NCBI__GCF_001431535.1:WP_057509361.1 346 AGEPG-HVNFDTIPWVIYTEPELAWVGKTEQQLKAEGIPYKAGSFPFAANGRAVAMIEPTGFVKVLAHA 413 **887.9************************************************************** PP TIGR01350 399 ktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaih 460 +t++ilG+h+vga++sel++e +l +e+ +++++la+++h+HP+lsE++++aa a++++aih lcl|NCBI__GCF_001431535.1:WP_057509361.1 414 ETDRILGMHLVGANVSELVHEGVLTMEFSGSADDLARICHAHPSLSEVVHDAAMAVSKRAIH 475 ************************************************************99 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: 10.24 // [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