Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate WP_093394376.1 BM091_RS06405 L-lactate dehydrogenase
Query= BRENDA::E7CXT1 (311 letters) >NCBI__GCF_900114975.1:WP_093394376.1 Length = 316 Score = 325 bits (832), Expect = 1e-93 Identities = 163/313 (52%), Positives = 224/313 (71%), Gaps = 5/313 (1%) Query: 3 KVAIIGSGFVGATSAFTLALSGTVTDIVLVDLNKDKAIGDALDISHGIPLIQPVNVYAGD 62 +V +IGSG VG+T AF L SG V +IVL+D N+D A G A+D+SHG+P + VYAG Sbjct: 4 RVIVIGSGAVGSTYAFALLQSGLVEEIVLLDQNRDLAAGQAMDLSHGLPFVLAARVYAGG 63 Query: 63 YKDVKGADVIVVTAGAAQKPGETRLDLVKKNTAIFKSMIPELLKYNDKAI-YLIVTNPVD 121 +D+K AD++V+TAGA Q+PG++RLDL+K N AI KS+ L K I ++VTNPVD Sbjct: 64 EEDLKDADMVVITAGAKQRPGQSRLDLLKVNAAIMKSIADSLEKQCGSEIPVMVVTNPVD 123 Query: 122 ILTYVTYKISGLPWGRVFGSGTVLDSSRFRYLLSKHCNIDPRNVHGRIIGEHGDTEFAAW 181 ++TY Y+ +G +FGSGTVLDS+RFRY+LS+HC +D R+VH +IGEHGD+E AW Sbjct: 124 VMTYALYRYTGWSRRLIFGSGTVLDSARFRYMLSRHCGVDSRSVHAYVIGEHGDSEVPAW 183 Query: 182 SITNISGISFNEYCSICGRVCNTN---FRKEVEEEVVNAAYKIIDKKGATYYAVAVAVRR 238 S+T+I+GI F+ YC C R CN + +K VEEEV N+AY IID KGAT++AVA+A+ R Sbjct: 184 SLTHIAGIPFDTYCGQCNR-CNEDREKVKKTVEEEVRNSAYHIIDYKGATWFAVALAMTR 242 Query: 239 IVECILRDENSILTVSSPLNGQYGVKDVSLSLPSIVGRNGVARILDLPLSDEEVEKFRHS 298 I +LR+E S+LTVS+ L G+YG+ D+ LS+P IVGRNG+ +I++ L D E E S Sbjct: 243 ITSAVLRNERSVLTVSTVLKGEYGLNDLCLSVPCIVGRNGIEQIIEADLKDPEKEALSLS 302 Query: 299 ASVMADVIKQLDI 311 A V+ +K+L + Sbjct: 303 AGVIHSAVKELSL 315 Lambda K H 0.319 0.137 0.394 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: 297 Number of extensions: 14 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: 311 Length of database: 316 Length adjustment: 27 Effective length of query: 284 Effective length of database: 289 Effective search space: 82076 Effective search space used: 82076 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_093394376.1 BM091_RS06405 (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.9687.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-112 361.6 0.0 1.9e-112 361.4 0.0 1.0 1 lcl|NCBI__GCF_900114975.1:WP_093394376.1 BM091_RS06405 L-lactate dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900114975.1:WP_093394376.1 BM091_RS06405 L-lactate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 361.4 0.0 1.9e-112 1.9e-112 1 298 [. 7 307 .. 7 308 .. 0.95 Alignments for each domain: == domain 1 score: 361.4 bits; conditional E-value: 1.9e-112 TIGR01771 1 iiGagaVGssvafalltqgladelvliDinedkaegealdlsdaasflkskvkvkagdyedlkdadlvv 69 +iG+gaVGs++afall++gl++e+vl+D n+d a g+a+dls++ +f+ ++v+ag edlkdad+vv lcl|NCBI__GCF_900114975.1:WP_093394376.1 7 VIGSGAVGSTYAFALLQSGLVEEIVLLDQNRDLAAGQAMDLSHGLPFV-LAARVYAGGEEDLKDADMVV 74 8***********************************************.668***************** PP TIGR01771 70 itaGaeqkpgetRlelveknvkilksivkevvks.gfdgillvvsNPvDiltyvvlklsglpkerviGs 137 itaGa+q+pg++Rl+l++ n++i+ksi++++ k+ g + ++vv+NPvD++ty++++++g +++ ++Gs lcl|NCBI__GCF_900114975.1:WP_093394376.1 75 ITAGAKQRPGQSRLDLLKVNAAIMKSIADSLEKQcGSEIPVMVVTNPVDVMTYALYRYTGWSRRLIFGS 143 *******************************987256666999************************** PP TIGR01771 138 GtvLdtaRlrrllaeklevdpksvhayvlGEHGdsevavwssakiagvplkelleekeke...kekelk 203 GtvLd+aR+r++l+ +++vd++svhayv+GEHGdsev++ws ++iag+p++ ++ + ++ ek +k lcl|NCBI__GCF_900114975.1:WP_093394376.1 144 GTVLDSARFRYMLSRHCGVDSRSVHAYVIGEHGDSEVPAWSLTHIAGIPFDTYCGQCNRCnedREKVKK 212 *****************************************************9877654211444556 PP TIGR01771 204 eiekevrdaayeiiekKgaTsygiglavariveailkdekrvlpvsallegeygikdvylgvPavlgkn 272 ++e+evr++ay+ii+ KgaT ++++la++ri++a+l++e++vl+vs++l+geyg +d++l+vP+++g+n lcl|NCBI__GCF_900114975.1:WP_093394376.1 213 TVEEEVRNSAYHIIDYKGATWFAVALAMTRITSAVLRNERSVLTVSTVLKGEYGLNDLCLSVPCIVGRN 281 9******************************************************************** PP TIGR01771 273 GveeilelkLseeEkeklkksaetlk 298 G+e+i+e++L++ Eke+l+ sa +++ lcl|NCBI__GCF_900114975.1:WP_093394376.1 282 GIEQIIEADLKDPEKEALSLSAGVIH 307 *********************98875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (299 nodes) Target sequences: 1 (316 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: 00:00:00.01 # Mc/sec: 7.46 // [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