Align L-lactate dehydrogenase; L-LDH; EC 1.1.1.27 (characterized)
to candidate WP_018231792.1 THITHI_RS0104045 L-lactate dehydrogenase
Query= SwissProt::Q5SJA1 (310 letters) >NCBI__GCF_000378965.1:WP_018231792.1 Length = 314 Score = 278 bits (710), Expect = 2e-79 Identities = 153/302 (50%), Positives = 199/302 (65%), Gaps = 1/302 (0%) Query: 3 VGIVGSGMVGSATAYALALLGVAREVVLVDLDRKLAQAHAEDILHATPFAHPVWVRAGSY 62 VGI+G+G VG A AYAL +A +VL+DLDR+ A+ A D++H V VRAG Y Sbjct: 6 VGIIGAGNVGMAAAYALFQRQIAGRLVLLDLDRRRAEGEAMDLMHGQALVGRVSVRAGDY 65 Query: 63 GDLEGARAVVLAAGVAQRPGETRLQLLDRNAQVFAQVVPRVLEAAPEAVLLVATNPVDVM 122 DL G + VV+ AGV Q+ GE+RL LL+RNA VF ++ + AP AVL+VATNPVD++ Sbjct: 66 ADLAGCQVVVICAGVGQQSGESRLDLLNRNAAVFREIAAELDRHAPGAVLVVATNPVDIL 125 Query: 123 TQVAYRLSGLPPGRVVGSGTILDTARFRALLAEYLRVAPQSVHAYVLGEHGDSEVLVWSS 182 T V RLS PP R+VG+GT+LDT+RFRALL EY V P+SVHAY+LGEHGDSEV +WSS Sbjct: 126 TAVMQRLSNRPPKRIVGTGTMLDTSRFRALLGEYYGVNPRSVHAYILGEHGDSEVPLWSS 185 Query: 183 AQVGGVPLLEFAEARGRALSPEDRARIDEGVRRAAYRIIEGKGATYYGIGAGLARLVRAI 242 A +GG +++ E GR + E VR AAY IIE KG T IG +A LVR I Sbjct: 186 AAIGGRTIVDH-EVNGRPFDAAAMQALFEQVRGAAYDIIERKGYTNTAIGLVIAYLVRVI 244 Query: 243 LTDEKGVYTVSAFTPEVEGVLEVSLSLPRILGAGGVEGTVYPSLSPEEREALRRSAEILK 302 L D+K V VS G+ +V LS+P ++G+GGVE V P LS +ER + SA +L+ Sbjct: 245 LEDQKSVLAVSIDPGSHYGLADVCLSIPCVVGSGGVECAVPPVLSDQERAGMHASAAVLR 304 Query: 303 EA 304 ++ Sbjct: 305 DS 306 Lambda K H 0.319 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: 293 Number of extensions: 10 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: 310 Length of database: 314 Length adjustment: 27 Effective length of query: 283 Effective length of database: 287 Effective search space: 81221 Effective search space used: 81221 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 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_018231792.1 THITHI_RS0104045 (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.22132.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-105 339.2 0.0 1.3e-105 339.0 0.0 1.0 1 lcl|NCBI__GCF_000378965.1:WP_018231792.1 THITHI_RS0104045 L-lactate dehyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000378965.1:WP_018231792.1 THITHI_RS0104045 L-lactate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 339.0 0.0 1.3e-105 1.3e-105 1 298 [. 8 304 .. 8 305 .. 0.97 Alignments for each domain: == domain 1 score: 339.0 bits; conditional E-value: 1.3e-105 TIGR01771 1 iiGagaVGssvafalltqgladelvliDinedkaegealdlsdaasflkskvkvkagdyedlkdadlvv 69 iiGag+VG+++a+al ++++a lvl+D+++ +aegea+dl+++++++ +v+v+agdy+dl++ ++vv lcl|NCBI__GCF_000378965.1:WP_018231792.1 8 IIGAGNVGMAAAYALFQRQIAGRLVLLDLDRRRAEGEAMDLMHGQALV-GRVSVRAGDYADLAGCQVVV 75 8***********************************************.779***************** PP TIGR01771 70 itaGaeqkpgetRlelveknvkilksivkevvksgfdgillvvsNPvDiltyvvlklsglpkerviGsG 138 i+aG q+ ge+Rl+l+++n++++++i+ e+ +++ ++l+v++NPvDilt v+++ls+ p++r++G+G lcl|NCBI__GCF_000378965.1:WP_018231792.1 76 ICAGVGQQSGESRLDLLNRNAAVFREIAAELDRHAPGAVLVVATNPVDILTAVMQRLSNRPPKRIVGTG 144 ********************************************************************* PP TIGR01771 139 tvLdtaRlrrllaeklevdpksvhayvlGEHGdsevavwssakiagvplkelleekekekekelkeiek 207 t+Ldt+R+r+ll+e ++v+p+svhay+lGEHGdsev++wssa i+g ++ + + + + + ++++ + lcl|NCBI__GCF_000378965.1:WP_018231792.1 145 TMLDTSRFRALLGEYYGVNPRSVHAYILGEHGDSEVPLWSSAAIGGRTIVDHEVNGRPFDAAAMQALFE 213 ***************************************************99866554556666**** PP TIGR01771 208 evrdaayeiiekKgaTsygiglavariveailkdekrvlpvsallegeygikdvylgvPavlgknGvee 276 +vr aay+iie+Kg+T+ +igl +a +v+ il+d+k+vl vs+ ++yg dv+l++P+v+g+ Gve lcl|NCBI__GCF_000378965.1:WP_018231792.1 214 QVRGAAYDIIERKGYTNTAIGLVIAYLVRVILEDQKSVLAVSIDPGSHYGLADVCLSIPCVVGSGGVEC 282 ********************************************************************* PP TIGR01771 277 ilelkLseeEkeklkksaetlk 298 + Ls++E++ ++ sa++l+ lcl|NCBI__GCF_000378965.1:WP_018231792.1 283 AVPPVLSDQERAGMHASAAVLR 304 *******************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (299 nodes) Target sequences: 1 (314 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.17 // [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