Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate PfGW456L13_4267 Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenase (EC 1.8.1.4)
Query= CharProtDB::CH_015561 (478 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 Length = 478 Score = 854 bits (2207), Expect = 0.0 Identities = 436/478 (91%), Positives = 455/478 (95%) Query: 1 MTQKFDVVVIGAGPGGYVAAIKAAQLGLKTACIEKYTDAEGKLALGGTCLNVGCIPSKAL 60 M+QKFDVVVIGAGPGGYVAAIKAAQLGL TACIEKYTD EGKLALGGTCLNVGCIPSKAL Sbjct: 1 MSQKFDVVVIGAGPGGYVAAIKAAQLGLSTACIEKYTDKEGKLALGGTCLNVGCIPSKAL 60 Query: 61 LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTSIQG 120 LDSSWK+ EA++ F +HGI+ V MDV AMVGRKA IVK LT GVATLFKANGVTSIQG Sbjct: 61 LDSSWKFHEAQDGFAIHGINHAGVTMDVPAMVGRKANIVKGLTSGVATLFKANGVTSIQG 120 Query: 121 HGKLLAGKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGALEFQAV 180 HGKLLAGKKVEVTK DG+ E+IEAENVILA GSRPIDIPPAPVDQNVIVDSTGALEFQ+V Sbjct: 121 HGKLLAGKKVEVTKPDGSVEIIEAENVILAPGSRPIDIPPAPVDQNVIVDSTGALEFQSV 180 Query: 181 PKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQGLDIK 240 PKRLGVIGAGVIGLELGSVW+RLGAEVTVLEALDTFLMAADTAVSKEA KTLTKQGLDIK Sbjct: 181 PKRLGVIGAGVIGLELGSVWSRLGAEVTVLEALDTFLMAADTAVSKEALKTLTKQGLDIK 240 Query: 241 LGARVTGSKVNGNEVEVTYTNAEGEQKITFDKLIVAVGRRPVTTDLLAADSGVTIDERGY 300 LGARVTGSKVNG+EV V YT+A+GEQ ITFDKLIVAVGRRPVTTDLLAAD GVT+DERG+ Sbjct: 241 LGARVTGSKVNGDEVVVNYTDAKGEQNITFDKLIVAVGRRPVTTDLLAADCGVTLDERGF 300 Query: 301 IFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH 360 + VDD+CAT+VPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH Sbjct: 301 VHVDDHCATTVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH 360 Query: 361 PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI 420 PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI Sbjct: 361 PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI 420 Query: 421 GPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKKR 478 GPSAAELVQQGAI MEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIH+ANRKKR Sbjct: 421 GPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHIANRKKR 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: 890 Number of extensions: 18 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 PfGW456L13_4267 (Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenase (EC 1.8.1.4))
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.18413.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.3e-165 534.7 10.5 1.1e-164 534.5 10.5 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 Dihydrolipoamide dehydrogenase o Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenas # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 534.5 10.5 1.1e-164 1.1e-164 1 461 [] 4 472 .. 4 472 .. 0.97 Alignments for each domain: == domain 1 score: 534.5 bits; conditional E-value: 1.1e-164 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvek..ek.....lGGtClnvGCiPtK 48 ++dvvviG+GpgGYvaAi+aaqlgl++a++ek +k lGGtClnvGCiP+K lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 4 KFDVVVIGAGPGGYVAAIKAAQLGLSTACIEKytDKegklaLGGTCLNVGCIPSK 58 59*****************************95421344449************* PP TIGR01350 49 alLksaevveelke.akelgievenvkldlekllerkekvvkklvgGvkaLlkkn 102 alL s+ ++e+++ ++ +gi+ ++v++d+ +++ rk ++vk l++Gv++L+k n lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 59 ALLDSSWKFHEAQDgFAIHGINHAGVTMDVPAMVGRKANIVKGLTSGVATLFKAN 113 ******************************************************* PP TIGR01350 103 kvevikGeaklldkkevevkkekke.kkleakniiiAtGseprelplkleedekv 156 +v++i+G++kll k+vev+k +++ + +ea+n+i+A Gs+p+ +p +d++v lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 114 GVTSIQGHGKLLAGKKVEVTKPDGSvEIIEAENVILAPGSRPIDIPP-APVDQNV 167 *********************9988899******************9.8999999 PP TIGR01350 157 vitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpalda 211 +++s++ale+++vp++l ++G+GviG+E++s++++lG++vtv+e+ld+ l a d+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 168 IVDSTGALEFQSVPKRLGVIGAGVIGLELGSVWSRLGAEVTVLEALDTFLMAADT 222 ******************************************************* PP TIGR01350 212 evskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvav 265 vsk++ k+l+k+g++i+ +a+vt + + devvv+ + +++++ +k++vav lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 223 AVSKEALKTLTKQGLDIKLGARVTGSKVNGDEVVVNYTDAkGEQNITFDKLIVAV 277 ************************99999999996666554679*********** PP TIGR01350 266 GrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAsk 320 Gr+p +++l + gv+lderg+++vd+++ t+vpg+yaiGDv++++mLAh+As+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 278 GRRPVTTDLLAADCGVTLDERGFVHVDDHCATTVPGVYAIGDVVRGMMLAHKASE 332 ******************************************************* PP TIGR01350 321 egvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfp 375 eg++++e+i g+++ +++y+++Psviyt+Pe+a vG+te+ +k+eg+ev+vg fp lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 333 EGIMVVERIKGHKA-QMNYDLIPSVIYTHPEIAWVGKTEQALKAEGVEVNVGTFP 386 ***********665.9*************************************** PP TIGR01350 376 faangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltv 430 faa+g+a+a+++t Gfvkvi+d kt+++lG+h++g++a+el+++ a+ +e+++++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 387 FAASGRAMAANDTGGFVKVIADAKTDRVLGVHVIGPSAAELVQQGAIGMEFGTSA 441 ******************************************************* PP TIGR01350 431 eelaktihpHPtlsEaikeaalaalgkaihv 461 e+l ++++ HPtlsEa++eaala++g aih+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4267 442 EDLGMMVFSHPTLSEALHEAALAVNGGAIHI 472 *****************************95 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10.92 // [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