Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate CCNA_00346 CCNA_00346 dihydrolipoamide dehydrogenase
Query= BRENDA::A0A0H2ZHZ0 (467 letters) >FitnessBrowser__Caulo:CCNA_00346 Length = 466 Score = 643 bits (1658), Expect = 0.0 Identities = 311/465 (66%), Positives = 377/465 (81%) Query: 2 MESYDVIVIGAGPGGYNAAIRAGQLGLKVACVEGRETLGGTCLNVGCMPSKALLHASELY 61 M YDV++IG GPGGYNAAIRAGQLGLKVA VEGR LGGTCLNVGCMPSKALLHASELY Sbjct: 1 MAQYDVVIIGGGPGGYNAAIRAGQLGLKVAIVEGRGKLGGTCLNVGCMPSKALLHASELY 60 Query: 62 AAASGGEFARLGIRVSPELDLAQMMKQKDESVAALTRGVEFLFRKHKVQWIKGWARLQGE 121 AAA+G EFA+LGI V P+L+L+QMM QK ESV ALT+GVEFL +K+KV+++KGW R+ G Sbjct: 61 AAATGPEFAKLGIEVKPKLNLSQMMAQKAESVEALTKGVEFLMKKNKVEYVKGWGRIDGV 120 Query: 122 GRVGVALADGGHAQLEARDIVIATGSEPAPLPGVPVDNQRILDSTGALELAEVPRHLVVI 181 G+V V DG LE ++IVIATGSEP PLPGV VDN+RI+DSTGAL L EVP+ LVV+ Sbjct: 121 GKVVVKAEDGSETTLETKNIVIATGSEPTPLPGVSVDNKRIIDSTGALSLPEVPKRLVVV 180 Query: 182 GAGVIGLELGSVWRRLGAQVTVLEYLERICPGLDGETARTLQRALTRQGMRFRLGTRVVA 241 GAGVIGLELGSVW+RLGA+VTV+EYL+RI PG D E A Q+ L +QG +F+LG +V Sbjct: 181 GAGVIGLELGSVWKRLGAEVTVVEYLDRILPGTDTEVANAFQKILVKQGFKFQLGAKVTG 240 Query: 242 ARSGEQGVELDLQPAAGGATESLQADYVLVAIGRRPYTEGLGLETVGLASDRRGMLENQG 301 A +G +GV+L +P AGG ++++ADYVLVAIGRRPYT+GLGLETVG+ D+RGM+ N Sbjct: 241 AEAGAKGVKLSFEPVAGGEAQTIEADYVLVAIGRRPYTQGLGLETVGVTPDKRGMIANDH 300 Query: 302 QRSAAPGVWVIGDVTSGPMLAHKAEEEAIVCIERIAGHAAEMNAEVIPSVIYTQPEVASV 361 ++ GVWVIGDVTSGPMLAHKAE+E + CIE IAG A +N +IP V+YT PEVA+V Sbjct: 301 FKTGVAGVWVIGDVTSGPMLAHKAEDEGVACIEMIAGKAGHVNYGIIPGVVYTSPEVATV 360 Query: 362 GLGEEQLQAARREYKVGRFPFSANSRAKINHESEGFIKILSDARSDQVLGVHMIGPGVSE 421 G E++L+A YKVG+FPF ANSRAKINHE++GF+KIL+DA++D++LG HMIGP V + Sbjct: 361 GKTEDELKAEGVAYKVGKFPFLANSRAKINHETDGFVKILADAKTDRILGAHMIGPNVGD 420 Query: 422 MIGEACVAMEFSASAEDLALTCHPHPTRSEALRQAAMDVHGRAMQ 466 MI E CVAMEF ++ED+A TCHPHPTRSEALRQAAM V G MQ Sbjct: 421 MIAEYCVAMEFGGASEDVARTCHPHPTRSEALRQAAMGVEGWTMQ 465 Lambda K H 0.318 0.135 0.390 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: 794 Number of extensions: 27 Number of successful extensions: 1 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: 467 Length of database: 466 Length adjustment: 33 Effective length of query: 434 Effective length of database: 433 Effective search space: 187922 Effective search space used: 187922 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 (21.7 bits) S2: 51 (24.3 bits)
Align candidate CCNA_00346 CCNA_00346 (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.30884.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-168 547.0 7.7 1.9e-168 546.8 7.7 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_00346 CCNA_00346 dihydrolipoamide dehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_00346 CCNA_00346 dihydrolipoamide dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 546.8 7.7 1.9e-168 1.9e-168 1 456 [. 3 461 .. 3 466 .] 0.96 Alignments for each domain: == domain 1 score: 546.8 bits; conditional E-value: 1.9e-168 TIGR01350 1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke..akelgiev 70 +ydvv+iGgGpgGY aAira+qlglkva+ve klGGtClnvGC+P+KalL+++e+++ ++ +++lgiev lcl|FitnessBrowser__Caulo:CCNA_00346 3 QYDVVIIGGGPGGYNAAIRAGQLGLKVAIVEGrGKLGGTCLNVGCMPSKALLHASELYAAATGpeFAKLGIEV 75 69*****************************879*************************9987679*****98 PP TIGR01350 71 envkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGse 142 + kl+l++++++k + v+ l++Gv++L+kknkve +kG +++ + ++v vk+e+++ ++le+kni+iAtGse lcl|FitnessBrowser__Caulo:CCNA_00346 76 -KPKLNLSQMMAQKAESVEALTKGVEFLMKKNKVEYVKGWGRIDGVGKVVVKAEDGSeTTLETKNIVIATGSE 147 .79**************************************************99886899************ PP TIGR01350 143 prelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevsk 215 p+ lp+ +++d+k++i+s++al+l+evp++lv+vG+GviG+E++s++++lG++vtv+e+ldrilp +d+ev++ lcl|FitnessBrowser__Caulo:CCNA_00346 148 PTPLPG-VSVDNKRIIDSTGALSLPEVPKRLVVVGAGVIGLELGSVWKRLGAEVTVVEYLDRILPGTDTEVAN 219 ******.999999************************************************************ PP TIGR01350 216 vlkkklkkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnleelgleklgvelde 285 + +k l k+g k+ +akvt e+ ++ v+ +e + e++t+ea++vLva+Gr+p +++lgle++gv+ d+ lcl|FitnessBrowser__Caulo:CCNA_00346 220 AFQKILVKQGFKFQLGAKVTGAEAGAKGVKlsFEPVAGgEAQTIEADYVLVAIGRRPYTQGLGLETVGVTPDK 292 ********************99999999995555444459********************************* PP TIGR01350 286 rgaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlt 358 rg+i +++++t v+g+++iGDv++++mLAh+A++egv ++e iagk+ +++y +P v+yt+Peva+vG+t lcl|FitnessBrowser__Caulo:CCNA_00346 293 RGMI-ANDHFKTGVAGVWVIGDVTSGPMLAHKAEDEGVACIEMIAGKAG-HVNYGIIPGVVYTSPEVATVGKT 363 **76.699**************************************998.9********************** PP TIGR01350 359 eeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltve 431 e+++k+eg+++kvgkfpf an++a + +etdGfvk+++d kt++ilGah++g+++ ++i+e +a+e+++ +e lcl|FitnessBrowser__Caulo:CCNA_00346 364 EDELKAEGVAYKVGKFPFLANSRAKINHETDGFVKILADAKTDRILGAHMIGPNVGDMIAEYCVAMEFGGASE 436 ************************************************************************* PP TIGR01350 432 elaktihpHPtlsEaikeaalaalg 456 ++a+t+hpHPt sEa+ +aa + g lcl|FitnessBrowser__Caulo:CCNA_00346 437 DVARTCHPHPTRSEALRQAAMGVEG 461 *******************987765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (466 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 6.57 // [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