Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate WP_015739554.1 ADEG_RS07980 L-lactate dehydrogenase
Query= BRENDA::B9MKZ8 (314 letters) >NCBI__GCF_000024605.1:WP_015739554.1 Length = 309 Score = 316 bits (810), Expect = 4e-91 Identities = 156/300 (52%), Positives = 210/300 (70%), Gaps = 2/300 (0%) Query: 6 KIVIIGTGFVGSSTAFALVDAGLATELVLIDVNRAKAEGEAMDLNHGISFVKPVKIWAGD 65 KI IIGTG VG++ A+AL+ +GL E+VLIDVNRAKAEGEA+DL +F PVK++AGD Sbjct: 3 KIAIIGTGSVGATAAYALIASGLGEEIVLIDVNRAKAEGEALDLGDSTAFTTPVKVYAGD 62 Query: 66 YEDCKDADIIIITAGANQKPGETRLDLTYKNAQITKSIIENIIKYTHDAILLMVTNPVDV 125 Y D DAD+II AGANQ+PGETRLDLT +N + K + + + ILLMVTNPVDV Sbjct: 63 YPDASDADLIIFAAGANQRPGETRLDLTQRNVAVLKEVAGKLAVHWRGGILLMVTNPVDV 122 Query: 126 LTYVMYKVSGLPKNQVIGSGTVLDSSRFRYLLAQHCQVDVRNVHAYILGEHGDSEIAAWS 185 LTYV ++ L +++G+GT+LDS+RFRY L+QH VD RN+HAY++GEHGD+ + WS Sbjct: 123 LTYVASRLLDLDPQRILGTGTILDSARFRYALSQHTGVDARNLHAYVIGEHGDTAVLLWS 182 Query: 186 LTNIGGVNFMQECLLCGKNCSPEVKEQIFNKVKNAAYEIIERKGATYYAIALAVRRIVEA 245 + G+ C G N P KEQI V+ AAY IIERKGATYYAI L +RR+ EA Sbjct: 183 RATVAGIPLEDFCRQRGLN--PPDKEQIDRYVRQAAYRIIERKGATYYAIGLGIRRLCEA 240 Query: 246 IIRDENSILPVSSIVDDVYGVKDVAISLPAIINKSGVVKVFDIPLTDEEKEKLKNSAQVI 305 I+++++S+L V+ V+ YG K VA SLP I+ + G + ++PL+ +E+E+LK S + Sbjct: 241 ILKNQHSVLTVTGPVEGTYGYKGVAFSLPTIVGREGRLFSLELPLSPQEEEELKRSVDTL 300 Lambda K H 0.318 0.136 0.384 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: 299 Number of extensions: 8 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: 314 Length of database: 309 Length adjustment: 27 Effective length of query: 287 Effective length of database: 282 Effective search space: 80934 Effective search space used: 80934 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: 48 (23.1 bits)
Align candidate WP_015739554.1 ADEG_RS07980 (L-lactate dehydrogenase)
to HMM TIGR01771 (L-lactate dehydrogenase (EC 1.1.1.27))
# 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/TIGR01771.hmm # target sequence database: /tmp/gapView.17448.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01771 [M=299] Accession: TIGR01771 Description: L-LDH-NAD: L-lactate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-112 359.5 0.0 8.5e-112 359.3 0.0 1.0 1 lcl|NCBI__GCF_000024605.1:WP_015739554.1 ADEG_RS07980 L-lactate dehydroge Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024605.1:WP_015739554.1 ADEG_RS07980 L-lactate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 359.3 0.0 8.5e-112 8.5e-112 1 298 [. 6 301 .. 6 302 .. 0.98 Alignments for each domain: == domain 1 score: 359.3 bits; conditional E-value: 8.5e-112 TIGR01771 1 iiGagaVGssvafalltqgladelvliDinedkaegealdlsdaasflkskvkvkagdyedlkdadlvv 69 iiG+g+VG+++a+al+ +gl +e+vliD+n+ kaegealdl d+++f+ ++vkv+agdy d++dadl++ lcl|NCBI__GCF_000024605.1:WP_015739554.1 6 IIGTGSVGATAAYALIASGLGEEIVLIDVNRAKAEGEALDLGDSTAFT-TPVKVYAGDYPDASDADLII 73 8***********************************************.99****************** PP TIGR01771 70 itaGaeqkpgetRlelveknvkilksivkevvksgfdgillvvsNPvDiltyvvlklsglpkerviGsG 138 +aGa+q+pgetRl+l ++nv++lk+++ ++ + gill+v+NPvD+ltyv+++l +l+++r++G+G lcl|NCBI__GCF_000024605.1:WP_015739554.1 74 FAAGANQRPGETRLDLTQRNVAVLKEVAGKLAVHWRGGILLMVTNPVDVLTYVASRLLDLDPQRILGTG 142 ********************************************************************* PP TIGR01771 139 tvLdtaRlrrllaeklevdpksvhayvlGEHGdsevavwssakiagvplkelleekekekekelkeiek 207 t+Ld+aR+r++l+++++vd+++ hayv+GEHGd++v +ws+a++ag+pl++++++++ + ++++i++ lcl|NCBI__GCF_000024605.1:WP_015739554.1 143 TILDSARFRYALSQHTGVDARNLHAYVIGEHGDTAVLLWSRATVAGIPLEDFCRQRGL-NPPDKEQIDR 210 *****************************************************98866.667778**** PP TIGR01771 208 evrdaayeiiekKgaTsygiglavariveailkdekrvlpvsallegeygikdvylgvPavlgknGvee 276 vr+aay+iie+KgaT+y+igl++ r++eailk++++vl+v+ +eg+yg+k+v++++P+++g++G lcl|NCBI__GCF_000024605.1:WP_015739554.1 211 YVRQAAYRIIERKGATYYAIGLGIRRLCEAILKNQHSVLTVTGPVEGTYGYKGVAFSLPTIVGREGRLF 279 ********************************************************************* PP TIGR01771 277 ilelkLseeEkeklkksaetlk 298 lel+Ls++E+e+lk+s++tl lcl|NCBI__GCF_000024605.1:WP_015739554.1 280 SLELPLSPQEEEELKRSVDTLL 301 ******************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (299 nodes) Target sequences: 1 (309 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: 00:00:00.01 # Mc/sec: 6.70 // [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