Align L-lactate dehydrogenase; L-LDH; EC 1.1.1.27 (characterized)
to candidate WP_034526999.1 LOSG293_RS03320 L-lactate dehydrogenase
Query= SwissProt::P56511 (320 letters) >NCBI__GCF_000740055.1:WP_034526999.1 Length = 310 Score = 344 bits (883), Expect = 1e-99 Identities = 174/304 (57%), Positives = 224/304 (73%), Gaps = 3/304 (0%) Query: 9 KVVLVGDGAVGSSYAFAMAQQGIAEEFVIVDVVKDRTKGDALDLEDAQAFTAPKKIYSGE 68 KV+LVGDGAVGSS+AF++ Q G +E VIVD+ KD T GDALDLED F+ + +G+ Sbjct: 7 KVILVGDGAVGSSFAFSILQSGGVDELVIVDIKKDHTMGDALDLEDITPFSGSATVRTGD 66 Query: 69 YSDCKDADLVVITAGAPQKPGESRLDLVNKNLNILSSIVKPVVDSGFDGIFLVAANPVDI 128 YSD +A +VVITAG P+KPGE+RLDLV KN IL SI+ PVV SGF G F+V+ANPVDI Sbjct: 67 YSDASEAQIVVITAGVPRKPGETRLDLVEKNTKILESIISPVVQSGFKGCFVVSANPVDI 126 Query: 129 LTYATWKFSGFPKERVIGSGTSLDSSRLRVALGKQFNVDPRSVDAYIMGEHGDSEFAAYS 188 LT T + SGFPKERVIG+GTSLDS+RL+VAL + +VD R ++AY++GEHGDS FA + Sbjct: 127 LTTMTQRLSGFPKERVIGTGTSLDSARLQVALAHKLDVDVREINAYVLGEHGDSSFANFD 186 Query: 189 TATIGTRPVRDVAKEQGVSDDDLAKLEDGVRNKAYDIINLKGATFYGIGTALMRISKAIL 248 A + +RD+ Q ++DDDL +LE V+ K II KGATFYG+ +L I KAIL Sbjct: 187 EAKVAGEAIRDI---QNITDDDLLELESEVKKKGGKIIGYKGATFYGVAMSLGIICKAIL 243 Query: 249 RDENAVLPVGAYMDGQYGLNDIYIGTPAIIGGTGLKQIIESPLSADELKKMQDSAATLKK 308 +E+ VLPV A +DGQYGL +IY+GT +II G G++Q++E PLS +E KKMQ SA + K Sbjct: 244 MNEDLVLPVSAPLDGQYGLKNIYLGTVSIINGNGIQQVLEVPLSEEETKKMQHSAYEMNK 303 Query: 309 VLND 312 VL + Sbjct: 304 VLEE 307 Lambda K H 0.315 0.134 0.375 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: 337 Number of extensions: 14 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: 320 Length of database: 310 Length adjustment: 27 Effective length of query: 293 Effective length of database: 283 Effective search space: 82919 Effective search space used: 82919 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: 42 (22.0 bits) S2: 48 (23.1 bits)
Align candidate WP_034526999.1 LOSG293_RS03320 (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.2881572.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-108 349.2 0.7 1.2e-108 349.0 0.7 1.0 1 NCBI__GCF_000740055.1:WP_034526999.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000740055.1:WP_034526999.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 349.0 0.7 1.2e-108 1.2e-108 1 298 [. 10 302 .. 10 303 .. 0.98 Alignments for each domain: == domain 1 score: 349.0 bits; conditional E-value: 1.2e-108 TIGR01771 1 iiGagaVGssvafalltqgladelvliDinedkaegealdlsdaasflkskvkvkagdyedlkdadlvvitaG 73 ++G+gaVGss+af++l++g +delv++Di++d++ g+aldl+d ++f+ +++v++gdy+d+++a++vvitaG NCBI__GCF_000740055.1:WP_034526999.1 10 LVGDGAVGSSFAFSILQSGGVDELVIVDIKKDHTMGDALDLEDITPFS-GSATVRTGDYSDASEAQIVVITAG 81 69**********************************************.5589******************** PP TIGR01771 74 aeqkpgetRlelveknvkilksivkevvksgfdgillvvsNPvDiltyvvlklsglpkerviGsGtvLdtaRl 146 + kpgetRl+lvekn+kil+si++ vv+sgf+g ++v +NPvDilt+++++lsg+pkerviG+Gt+Ld+aRl NCBI__GCF_000740055.1:WP_034526999.1 82 VPRKPGETRLDLVEKNTKILESIISPVVQSGFKGCFVVSANPVDILTTMTQRLSGFPKERVIGTGTSLDSARL 154 ************************************************************************* PP TIGR01771 147 rrllaeklevdpksvhayvlGEHGdsevavwssakiagvplkelleekekekekelkeiekevrdaayeiiek 219 +++la+kl+vd ++++ayvlGEHGds++a +++ak+ag ++++++ + +++l e+e+ev++++ +ii NCBI__GCF_000740055.1:WP_034526999.1 155 QVALAHKLDVDVREINAYVLGEHGDSSFANFDEAKVAGEAIRDIQNIT----DDDLLELESEVKKKGGKIIGY 223 ********************************************9865....77889**************** PP TIGR01771 220 KgaTsygiglavariveailkdekrvlpvsallegeygikdvylgvPavlgknGveeilelkLseeEkeklkk 292 KgaT+yg+++++ i++ail +e+ vlpvsa l+g+yg k++ylg+ ++++ nG++++le++LseeE++k+++ NCBI__GCF_000740055.1:WP_034526999.1 224 KGATFYGVAMSLGIICKAILMNEDLVLPVSAPLDGQYGLKNIYLGTVSIINGNGIQQVLEVPLSEEETKKMQH 296 ************************************************************************* PP TIGR01771 293 saetlk 298 sa ++ NCBI__GCF_000740055.1:WP_034526999.1 297 SAYEMN 302 *98775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (299 nodes) Target sequences: 1 (310 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: 00:00:00.00 # Mc/sec: 20.71 // [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