Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate Dsui_2219 Dsui_2219 dihydrolipoamide dehydrogenase
Query= SwissProt::P14218 (478 letters) >FitnessBrowser__PS:Dsui_2219 Length = 474 Score = 508 bits (1308), Expect = e-148 Identities = 267/478 (55%), Positives = 340/478 (71%), Gaps = 12/478 (2%) Query: 1 MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEK--YIGKEGKVALGGTCLNVGCIPSK 58 MS++FDV+VIG GPGGYVAAIRAAQLG AC E Y +G+ LGGTCLNVGCIPSK Sbjct: 1 MSKQFDVLVIGGGPGGYVAAIRAAQLGFSVACCESNPYADPKGEPRLGGTCLNVGCIPSK 60 Query: 59 ALLDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSF 118 ALL +S+ + EA AF GI+ IDVP M+ RK +V LT GI LFK N VT Sbjct: 61 ALLHTSHLFEEAGHAFAAQGIQVSAPKIDVPTMIGRKTAVVTQLTSGIKGLFKKNKVTQL 120 Query: 119 EGHGKLL----ANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGA 174 GHG + A QV+V +V+EA+ VI+A+GS+ +P + I++D+ GA Sbjct: 121 NGHGSFVGQGGAGWQVKVGD-----EVVEAKQVIVATGSKARHLPGIAVDQKIVLDNEGA 175 Query: 175 LEFQAVPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTK 234 LE Q+VPKKL +IGAGVIGLE+GSVW RLG+EVT+LEA FL AAD+ +AKEALK+ TK Sbjct: 176 LEQQSVPKKLAIIGAGVIGLEMGSVWRRLGSEVTILEASPDFLAAADQDVAKEALKLFTK 235 Query: 235 QGLNIRLGARVTASEVKKKQVTVTFTDANG-EQKETFDKLIVAVGRRPVTTDLLAADSGV 293 QGLNI++G ++ ++V KK V++ +TD +G EQK ++LIV+VGR P T L A G+ Sbjct: 236 QGLNIQMGVKLGETKVSKKGVSIAYTDKDGKEQKLDAERLIVSVGRVPNTDGLNAEKIGL 295 Query: 294 TLDERGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLI 353 L+ERG I VD HC+T++PGV+A+GDVV G MLAHKA EE VMVAE +AG N+D I Sbjct: 296 KLNERGQIEVDGHCRTNLPGVWAVGDVVSGPMLAHKAMEEAVMVAELMAGQAGHCNFDTI 355 Query: 354 PSVIYTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDR 413 P VIYT PEIAWVGKTEQ LKA+GV G PF A+GRA+ D TG VK++A AKTDR Sbjct: 356 PWVIYTSPEIAWVGKTEQQLKADGVAYKAGKIPFLANGRALGMGDPTGFVKMLACAKTDR 415 Query: 414 VLGVHVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIH 471 +LGVH+IGP+A+EL+ + + MEFG ++EDL + +HPTLSEA+HEAALA + +H Sbjct: 416 ILGVHIIGPNASELIAEAVVTMEFGGASEDLARICHAHPTLSEAVHEAALACDKRPLH 473 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: 638 Number of extensions: 23 Number of successful extensions: 5 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: 474 Length adjustment: 33 Effective length of query: 445 Effective length of database: 441 Effective search space: 196245 Effective search space used: 196245 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 Dsui_2219 Dsui_2219 (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.21170.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-165 535.0 3.4 8.6e-165 534.8 3.4 1.0 1 lcl|FitnessBrowser__PS:Dsui_2219 Dsui_2219 dihydrolipoamide dehyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_2219 Dsui_2219 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 534.8 3.4 8.6e-165 8.6e-165 1 461 [] 4 474 .] 4 474 .] 0.96 Alignments for each domain: == domain 1 score: 534.8 bits; conditional E-value: 8.6e-165 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalveke.........klGGtClnvGCiPtKalLksaevveelke.akelg 67 ++dv+viGgGpgGYvaAiraaqlg++va+ e + +lGGtClnvGCiP+KalL++++++ee+ + ++ g lcl|FitnessBrowser__PS:Dsui_2219 4 QFDVLVIGGGPGGYVAAIRAAQLGFSVACCESNpyadpkgepRLGGTCLNVGCIPSKALLHTSHLFEEAGHaFAAQG 80 59*****************************6533333333369***************************99**** PP TIGR01350 68 ievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGsepr 144 i+v+ k+d+ ++ rk++vv++l++G+k+L+kknkv++++G++++++++ + + + +++eak++i+AtGs+ r lcl|FitnessBrowser__PS:Dsui_2219 81 IQVSAPKIDVPTMIGRKTAVVTQLTSGIKGLFKKNKVTQLNGHGSFVGQGGAGWQVKVGDEVVEAKQVIVATGSKAR 157 ************************************************99988888888899*************** PP TIGR01350 145 elplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkkl 221 +lp+ +++d+k+v+++e+ale ++vp++l+i+G+GviG+E++s++++lG++vt++e+++ l+a d++v+k++ k + lcl|FitnessBrowser__PS:Dsui_2219 158 HLPG-IAVDQKIVLDNEGALEQQSVPKKLAIIGAGVIGLEMGSVWRRLGSEVTILEASPDFLAAADQDVAKEALKLF 233 ****.************************************************************************ PP TIGR01350 222 kkkgvkiltnakvtevekeedevv..veakkkevetleaekvLvavGrkpnleelgleklgveldergaikvdeelr 296 +k+g++i ++ k+ e++ +++ v+ ++ k++++++l+ae+++v+vGr pn+++l+ ek+g++l+erg+i+vd ++r lcl|FitnessBrowser__PS:Dsui_2219 234 TKQGLNIQMGVKLGETKVSKKGVSiaYTDKDGKEQKLDAERLIVSVGRVPNTDGLNAEKIGLKLNERGQIEVDGHCR 310 *************966666555554377777789******************************************* PP TIGR01350 297 tnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgk 373 tn+pg++a+GDv++++mLAh+A++e+v++ae +ag++ +++ +++P viyt+Pe+a vG+te+q+k++g+++k+gk lcl|FitnessBrowser__PS:Dsui_2219 311 TNLPGVWAVGDVVSGPMLAHKAMEEAVMVAELMAGQAG-HCNFDTIPWVIYTSPEIAWVGKTEQQLKADGVAYKAGK 386 ***********************************998.9************************************* PP TIGR01350 374 fpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikea 450 +pf ang+al +++ +Gfvk+++ kt++ilG+hi+g++aseli+e+++ +e+++ +e+la+++h+HPtlsEa++ea lcl|FitnessBrowser__PS:Dsui_2219 387 IPFLANGRALGMGDPTGFVKMLACAKTDRILGVHIIGPNASELIAEAVVTMEFGGASEDLARICHAHPTLSEAVHEA 463 ***************************************************************************** PP TIGR01350 451 alaalgkaihv 461 ala ++++h+ lcl|FitnessBrowser__PS:Dsui_2219 464 ALACDKRPLHF 474 *****999995 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10.51 // [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