Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_011654335.1 RL_RS28930 dihydrolipoyl dehydrogenase
Query= reanno::Smeli:SMc03204 (464 letters) >NCBI__GCF_000009265.1:WP_011654335.1 Length = 465 Score = 648 bits (1671), Expect = 0.0 Identities = 326/465 (70%), Positives = 386/465 (83%), Gaps = 1/465 (0%) Query: 1 MKEISCKLLVLGAGPGGYVAAIRAGQLGVNTVIVEKAKAGGTCLNVGCIPSKALIHAADE 60 MKEI CKLLV+GAGPGGYV AIRAGQLGV+TVIVE K GGTCL VGCIPSKALIHAA+E Sbjct: 1 MKEIVCKLLVIGAGPGGYVCAIRAGQLGVDTVIVEAGKPGGTCLTVGCIPSKALIHAAEE 60 Query: 61 YHRLRAAASGKGPLGLSLSAPAIDLRRTIAWKDGIVGRLNGGVTGLLKKAGVKAVIGEGR 120 + + +GK P+G+ + +IDL RTIAWKDGIVGRL GV+GLL+KA VK V G Sbjct: 61 FDATQKMLAGKNPMGIRVEGASIDLGRTIAWKDGIVGRLTSGVSGLLQKARVKIVHGRAH 120 Query: 121 FVDGKTVDVETETGLQRIRAEAIVIATGSAPVELPDLPFGGSVISSTQALALTDVPQTLA 180 F DGKTV+VETETG Q IRAE +VIATGS PVEL +LPFGG VISST+AL+LT++P+ L Sbjct: 121 FRDGKTVEVETETGQQIIRAETVVIATGSDPVELSNLPFGGRVISSTEALSLTELPKKLV 180 Query: 181 VIGGGYIGLELGTAFAKLGSKVTVLEALDRILPQYDADLSKPVMKRLGELGVEVFTRTAA 240 V+GGGYIGLELGTAF+K+GS VTV+EA ++LPQYDA+L +PVM++L E + + T A Sbjct: 181 VVGGGYIGLELGTAFSKMGSDVTVVEATPQVLPQYDAELVRPVMRKLTEGSIRLLTGAKA 240 Query: 241 KRLSADRRGLLAEE-NGRAFEVPAEKVLVTVGRRPVTDGWGLEEIDLDHSGRFIRIDDQC 299 L+ + L+ E +GR +PA+++LVTVGRRP T G GLEE+DLD +G ++RIDD+C Sbjct: 241 IGLADNGEALIVEAADGRRESLPADRILVTVGRRPRTAGSGLEELDLDRAGPYLRIDDRC 300 Query: 300 RTSMRGVYAIGDVTGEPMLAHRAMAQGEMVAEIVAGHKRSWDKRCIPAVCFTDPEIVGAG 359 RTSMRG+YAIGDVTGEPMLAHRAMAQGEMVAEI+AG KR+WDKRCIPA+CFTDPEIV AG Sbjct: 301 RTSMRGIYAIGDVTGEPMLAHRAMAQGEMVAEIIAGKKRAWDKRCIPAICFTDPEIVSAG 360 Query: 360 LSPEEARAAGIDVKIGQFPFQANGRAMTTLSEDGFVRVIARADNHLVLGIQAVGHGVSEL 419 LSP +A+A G +++ GQFPF ANGRAMT LSE+GFVR++ARAD +LVLG+QAVG GVSEL Sbjct: 361 LSPADAKAQGYEIRTGQFPFSANGRAMTMLSEEGFVRIVARADTNLVLGLQAVGAGVSEL 420 Query: 420 SATFALAIEMGARLEDIAGTIHAHPTQSEAFQEAALKTLGHALHI 464 SA FALAIEMGARLEDIAGTIHAHPT+SEA EAALK LG ALHI Sbjct: 421 SAAFALAIEMGARLEDIAGTIHAHPTRSEAVMEAALKALGSALHI 465 Lambda K H 0.319 0.137 0.396 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: 728 Number of extensions: 24 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: 464 Length of database: 465 Length adjustment: 33 Effective length of query: 431 Effective length of database: 432 Effective search space: 186192 Effective search space used: 186192 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_011654335.1 RL_RS28930 (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.31302.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-155 503.1 0.4 3.9e-155 502.9 0.4 1.0 1 lcl|NCBI__GCF_000009265.1:WP_011654335.1 RL_RS28930 dihydrolipoyl dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009265.1:WP_011654335.1 RL_RS28930 dihydrolipoyl dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 502.9 0.4 3.9e-155 3.9e-155 4 461 .] 8 465 .] 5 465 .] 0.98 Alignments for each domain: == domain 1 score: 502.9 bits; conditional E-value: 3.9e-155 TIGR01350 4 vvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke....akelgi 68 ++viG+GpgGYv+Aira+qlg +++ve k GGtCl vGCiP+Kal+++ae ++ ++ ++ +gi lcl|NCBI__GCF_000009265.1:WP_011654335.1 8 LLVIGAGPGGYVCAIRAGQLGVDTVIVEAGKPGGTCLTVGCIPSKALIHAAEEFDATQKmlagKNPMGI 76 78**************************************************99987765323467*** PP TIGR01350 69 evenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniii 137 +ve+ ++dl + ++k+ +v +l++Gv++Ll+k++v+ ++G+a+++d k+vev++e++++ ++a++++i lcl|NCBI__GCF_000009265.1:WP_011654335.1 77 RVEGASIDLGRTIAWKDGIVGRLTSGVSGLLQKARVKIVHGRAHFRDGKTVEVETETGQQIIRAETVVI 145 ********************************************************************* PP TIGR01350 138 AtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldril 206 AtGs+p el+ l + + +vi+s+eal+l+e+p++lv+vGgG+iG+E++++f+k+G++vtv+e+++++l lcl|NCBI__GCF_000009265.1:WP_011654335.1 146 ATGSDPVELSN-LPFGG-RVISSTEALSLTELPKKLVVVGGGYIGLELGTAFSKMGSDVTVVEATPQVL 212 ***********.99998.7************************************************** PP TIGR01350 207 paldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelg 275 p+ dae+ + +++kl++ +++lt+ak + ++ +++ vea ++ e+l a+++Lv+vGr+p++ + g lcl|NCBI__GCF_000009265.1:WP_011654335.1 213 PQYDAELVRPVMRKLTEGSIRLLTGAKAIGLADNGEALIVEAADGRRESLPADRILVTVGRRPRTAGSG 281 ******************************************99999********************** PP TIGR01350 276 leklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPs 344 le+l+++ ++ +d+++rt++ giyaiGDv+g++mLAh+A+++g ++ae iagk++ + d++ +P+ lcl|NCBI__GCF_000009265.1:WP_011654335.1 282 LEELDLDRAG-PYLRIDDRCRTSMRGIYAIGDVTGEPMLAHRAMAQGEMVAEIIAGKKR-AWDKRCIPA 348 *******888.99*******************************************887.9******** PP TIGR01350 345 viytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaea 413 + +t+Pe+ s Gl+ ++ak++g+e+++g+fpf+ang+a+++ ++Gfv++++ +t+ +lG++ vga + lcl|NCBI__GCF_000009265.1:WP_011654335.1 349 ICFTDPEIVSAGLSPADAKAQGYEIRTGQFPFSANGRAMTMLSEEGFVRIVARADTNLVLGLQAVGAGV 417 ********************************************************************* PP TIGR01350 414 seliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461 sel + +ala+e+++++e++a tih+HPt sEa++eaal+alg+a+h+ lcl|NCBI__GCF_000009265.1:WP_011654335.1 418 SELSAAFALAIEMGARLEDIAGTIHAHPTRSEAVMEAALKALGSALHI 465 ********************************************9995 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (461 nodes) Target sequences: 1 (465 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: 00:00:00.02 # Mc/sec: 9.83 // [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