Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate SMc02487 SMc02487 dihydrolipoamide dehydrogenase
Query= BRENDA::Q9M5K2 (507 letters) >FitnessBrowser__Smeli:SMc02487 Length = 468 Score = 550 bits (1418), Expect = e-161 Identities = 270/465 (58%), Positives = 347/465 (74%), Gaps = 2/465 (0%) Query: 45 DVVIIGGGPGGYVAAIKAAQLGLKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 104 D+++IG GPGGYV AIKAAQLG+K +EKR GGTCLNVGCIPSKALLH+S M+H+A+ Sbjct: 4 DLIVIGSGPGGYVCAIKAAQLGMKVAVVEKRSTYGGTCLNVGCIPSKALLHASEMFHQAQ 63 Query: 105 HVFANHGVKVSSVEVDLPAMLAQKDTAVKNLTRGVEGLFKKNKVNYVKGYGKFLSPSEVS 164 H GV+V++ +++L M+A KD VK+ GV LFKKNK++ +G GK L +VS Sbjct: 64 HGLEALGVEVANPKLNLQKMMAHKDATVKSNVDGVSFLFKKNKIDGFQGTGKVLGQGKVS 123 Query: 165 VDTIDGENVVVKGKHIIVATGSDVKSLPGITI--DEKKIVSSTGALSLTEIPKKLIVIGA 222 V GE V++ K++++ATGSDV +PG+ + DEK IVSSTGAL+L ++P +IV+G Sbjct: 124 VTNEKGEEQVLEAKNVVIATGSDVAGIPGVEVAFDEKTIVSSTGALALEKVPASMIVVGG 183 Query: 223 GYIGLEMGSVWGRLGSEVTVVEFAADIVPAMDGEIRKQFQRSLEKQKMKFMLKTKVVGVD 282 G IGLE+GSVW RLG++VTVVEF I+ MDGE+ KQ QR L KQ + F L KV G Sbjct: 184 GVIGLELGSVWARLGAKVTVVEFLDTILGGMDGEVAKQLQRMLTKQGIDFKLGAKVTGAV 243 Query: 283 SSGDGVKLIVEPAEGGEQTTLEADVVLVSAGRTPFTSGLDLEKIGVETDKGGRILVNERF 342 SGDG K+ EP +GGE TTL+A+VVL++ GR P T GL L K GV D GR+ ++ F Sbjct: 244 KSGDGAKVTFEPVKGGEATTLDAEVVLIATGRKPSTDGLGLAKAGVVLDSRGRVEIDRHF 303 Query: 343 STNVSGVYAIGDVIPGPMLAHKAEEDGVACVEFIAGKHGHVDYDKVPGVVYTYPEVASVG 402 T+++GVYAIGDV+ GPMLAHKAE++GVA E IAG+ GHV+YD +PGVVYT PEVASVG Sbjct: 304 QTSIAGVYAIGDVVRGPMLAHKAEDEGVAVAEIIAGQAGHVNYDVIPGVVYTQPEVASVG 363 Query: 403 KTEEQLKKEGVSYNVGKFPFMANSRAKAIDTAEGMVKILADKETDKILGVHIMSPNAGEL 462 KTEE+LK GV+Y +GKFPF AN RA+A+ +G VKILADKETD++LG HI+ AGE+ Sbjct: 364 KTEEELKAAGVAYKIGKFPFTANGRARAMLQTDGFVKILADKETDRVLGGHIIGFGAGEM 423 Query: 463 IHEAVLAINYDASSEDIARVCHAHPTMSEAIKEAAMATYDKPIHM 507 IHE + + + SSED+ R CHAHPTMSEA+KEAA++T+ KPIHM Sbjct: 424 IHEIAVLMEFGGSSEDLGRTCHAHPTMSEAVKEAALSTFFKPIHM 468 Lambda K H 0.315 0.134 0.376 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: 666 Number of extensions: 31 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: 507 Length of database: 468 Length adjustment: 34 Effective length of query: 473 Effective length of database: 434 Effective search space: 205282 Effective search space used: 205282 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: 52 (24.6 bits)
Align candidate SMc02487 SMc02487 (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.12076.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-185 602.6 15.4 2.6e-185 602.4 15.4 1.0 1 lcl|FitnessBrowser__Smeli:SMc02487 SMc02487 dihydrolipoamide dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc02487 SMc02487 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 602.4 15.4 2.6e-185 2.6e-185 2 461 .] 3 468 .] 2 468 .] 0.97 Alignments for each domain: == domain 1 score: 602.4 bits; conditional E-value: 2.6e-185 TIGR01350 2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgievenvk 74 yd++viG+GpgGYv+Ai+aaqlg+kva+vek +++GGtClnvGCiP+KalL+++e+++++++ ++ lg+ev+n k lcl|FitnessBrowser__Smeli:SMc02487 3 YDLIVIGSGPGGYVCAIKAAQLGMKVAVVEKrSTYGGTCLNVGCIPSKALLHASEMFHQAQHgLEALGVEVANPK 77 9******************************999***************************************** PP TIGR01350 75 ldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGseprelpl 148 l+l+k++++k+++vk+ v+Gv++L+kknk++ ++G++k+l++++v+v++ek+e ++leakn++iAtGs+++ +p+ lcl|FitnessBrowser__Smeli:SMc02487 78 LNLQKMMAHKDATVKSNVDGVSFLFKKNKIDGFQGTGKVLGQGKVSVTNEKGEeQVLEAKNVVIATGSDVAGIPG 152 **************************************************9988999****************** PP TIGR01350 149 k.leedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklk 222 +++dek++++s++al+l++vp s+++vGgGviG+E++s++a+lG+kvtv+e+ld+il +d ev+k+l+++l+ lcl|FitnessBrowser__Smeli:SMc02487 153 VeVAFDEKTIVSSTGALALEKVPASMIVVGGGVIGLELGSVWARLGAKVTVVEFLDTILGGMDGEVAKQLQRMLT 227 99999********************************************************************** PP TIGR01350 223 kkgvkiltnakvt..evekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdee 294 k+g++++ +akvt + + ++v++e k+ e++tl+ae vL+a Grkp++++lgl+k gv ld+rg++++d++ lcl|FitnessBrowser__Smeli:SMc02487 228 KQGIDFKLGAKVTgaVKSGDGAKVTFEPVKGgEATTLDAEVVLIATGRKPSTDGLGLAKAGVVLDSRGRVEIDRH 302 *************7333445567778877777******************************************* PP TIGR01350 295 lrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegiev 369 ++t+++g+yaiGDv++++mLAh+A++egv +ae iag++ +++y+++P v+yt+PevasvG+tee++k++g+++ lcl|FitnessBrowser__Smeli:SMc02487 303 FQTSIAGVYAIGDVVRGPMLAHKAEDEGVAVAEIIAGQAG-HVNYDVIPGVVYTQPEVASVGKTEEELKAAGVAY 376 *************************************998.9********************************* PP TIGR01350 370 kvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtls 444 k+gkfpf+ang+a+a+ +tdGfvk+++dk+t+++lG hi+g a e+i+e+a+++e+++++e+l +t+h+HPt+s lcl|FitnessBrowser__Smeli:SMc02487 377 KIGKFPFTANGRARAMLQTDGFVKILADKETDRVLGGHIIGFGAGEMIHEIAVLMEFGGSSEDLGRTCHAHPTMS 451 *************************************************************************** PP TIGR01350 445 Eaikeaalaalgkaihv 461 Ea+keaal+++ k+ih+ lcl|FitnessBrowser__Smeli:SMc02487 452 EAVKEAALSTFFKPIHM 468 ****************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (468 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: 00:00:00.01 # Mc/sec: 10.85 // [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