Align L-lactate dehydrogenase; L-LDH; EC 1.1.1.27 (characterized)
to candidate WP_034526520.1 LOSG293_RS02225 L-lactate dehydrogenase
Query= SwissProt::Q59645 (323 letters) >NCBI__GCF_000740055.1:WP_034526520.1 Length = 319 Score = 506 bits (1304), Expect = e-148 Identities = 255/317 (80%), Positives = 279/317 (88%) Query: 1 MSNIQNHQKVVLVGDGAVGSSYAFAMAEEGIAEEFVIVDVVKVRTVGDALDLEDATPFTA 60 M+N + QKV+LVGDGAVGSSYAFAM +G+AEEFVIVDVVK RT GDALDLED FT+ Sbjct: 1 MTNAKKFQKVMLVGDGAVGSSYAFAMMHQGLAEEFVIVDVVKERTEGDALDLEDVQAFTS 60 Query: 61 PKNIYSGEYSDCKDADLVVITAGAPQKPGETRLDLVNKNLNILSTILKPVVDSGFDGIFL 120 PKN+YSGEYSD KDADLVVITAGAPQKPGETRLDLVNKNL ILSTI+KP+VDSGFDGIFL Sbjct: 61 PKNVYSGEYSDAKDADLVVITAGAPQKPGETRLDLVNKNLKILSTIVKPIVDSGFDGIFL 120 Query: 121 VAANPVDILTYATWKFSGFPKEKVIGSGISLDTARLRVALGKKFNVSPESVDAYILGEHG 180 +AANPVDILTYATWKFSGFPK KVIGSG SLDTARLR ALGKKFNV P +V+AYI+GEHG Sbjct: 121 IAANPVDILTYATWKFSGFPKNKVIGSGTSLDTARLRAALGKKFNVDPRNVEAYIMGEHG 180 Query: 181 DSEFAAYSSATIGTKPLLEIAKEEGVSTDELAEIEDSVRNKAYEIINKKGATFYGVGTAL 240 DSEFAAY ATIG+KPL+ IAKE GV+ DEL +IED R+KAYEIIN+KGATFYGV TAL Sbjct: 181 DSEFAAYDEATIGSKPLMTIAKENGVTKDELLKIEDETRHKAYEIINRKGATFYGVATAL 240 Query: 241 MRISKAILRDENAVLPVGAYMDGEYGLNDIYIGTPAVINGQGLNRVIEAPLSDDEKKKMT 300 MRISKAILRDENAVLPVGA +DGEYGLNDI+IGTPAVIN G+ VIE PLSD+EK KM Sbjct: 241 MRISKAILRDENAVLPVGAPLDGEYGLNDIFIGTPAVINANGIESVIEIPLSDEEKAKMA 300 Query: 301 DSATTLKKVLTDGLNAL 317 SA TLKKV DGL+AL Sbjct: 301 ASAETLKKVTKDGLDAL 317 Lambda K H 0.313 0.134 0.368 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: 458 Number of extensions: 8 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: 323 Length of database: 319 Length adjustment: 28 Effective length of query: 295 Effective length of database: 291 Effective search space: 85845 Effective search space used: 85845 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 bits)
Align candidate WP_034526520.1 LOSG293_RS02225 (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.1854677.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-132 425.8 0.0 5.2e-132 425.7 0.0 1.0 1 NCBI__GCF_000740055.1:WP_034526520.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000740055.1:WP_034526520.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 425.7 0.0 5.2e-132 5.2e-132 1 299 [] 12 308 .. 12 308 .. 0.98 Alignments for each domain: == domain 1 score: 425.7 bits; conditional E-value: 5.2e-132 TIGR01771 1 iiGagaVGssvafalltqgladelvliDinedkaegealdlsdaasflkskvkvkagdyedlkdadlvvitaG 73 ++G+gaVGss+afa+++qgla+e+v++D+ ++++eg+aldl+d ++f+ s+++v++g+y+d+kdadlvvitaG NCBI__GCF_000740055.1:WP_034526520.1 12 LVGDGAVGSSYAFAMMHQGLAEEFVIVDVVKERTEGDALDLEDVQAFT-SPKNVYSGEYSDAKDADLVVITAG 83 69**********************************************.889********************* PP TIGR01771 74 aeqkpgetRlelveknvkilksivkevvksgfdgillvvsNPvDiltyvvlklsglpkerviGsGtvLdtaRl 146 a+qkpgetRl+lv+kn+kil++ivk +v+sgfdgi+l+++NPvDilty+++k+sg+pk++viGsGt+LdtaRl NCBI__GCF_000740055.1:WP_034526520.1 84 APQKPGETRLDLVNKNLKILSTIVKPIVDSGFDGIFLIAANPVDILTYATWKFSGFPKNKVIGSGTSLDTARL 156 ************************************************************************* PP TIGR01771 147 rrllaeklevdpksvhayvlGEHGdsevavwssakiagvplkelleekekekekelkeiekevrdaayeiiek 219 r++l++k++vdp++v+ay++GEHGdse+a++++a+i+++pl +++e++ +++el +ie+e+r++ayeii++ NCBI__GCF_000740055.1:WP_034526520.1 157 RAALGKKFNVDPRNVEAYIMGEHGDSEFAAYDEATIGSKPLMTIAKENGV-TKDELLKIEDETRHKAYEIINR 228 *********************************************98876.666667**************** PP TIGR01771 220 KgaTsygiglavariveailkdekrvlpvsallegeygikdvylgvPavlgknGveeilelkLseeEkeklkk 292 KgaT+yg+++a++ri +ail+de++vlpv+a l+geyg +d+++g+Pav+++nG+e+++e++Ls+eEk+k++ NCBI__GCF_000740055.1:WP_034526520.1 229 KGATFYGVATALMRISKAILRDENAVLPVGAPLDGEYGLNDIFIGTPAVINANGIESVIEIPLSDEEKAKMAA 301 ************************************************************************* PP TIGR01771 293 saetlkk 299 saetlkk NCBI__GCF_000740055.1:WP_034526520.1 302 SAETLKK 308 *****96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (299 nodes) Target sequences: 1 (319 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 25.24 // [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