Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_017222083.1 A923_RS0112890 triose-phosphate isomerase
Query= SwissProt::P50921 (256 letters) >NCBI__GCF_000276805.1:WP_017222083.1 Length = 251 Score = 262 bits (670), Expect = 4e-75 Identities = 142/252 (56%), Positives = 171/252 (67%), Gaps = 2/252 (0%) Query: 1 MRHPVVMGNWKLNGSKEMVVDLLNGLNAELEGVTGVDVAVAPPALFVDLAERTLTEAGSA 60 MR +VMGNWKLN +K V L+NGL + V+VAV PPA+F+ E LT A +A Sbjct: 1 MRQALVMGNWKLNATKASVEALINGLVDAAKDNATVEVAVCPPAVFIPQVE-ALT-ADTA 58 Query: 61 IILGAQNTDLNNSGAFTGDMSPAMLKEFGATHIIIGHSERREYHAESDEFVAKKFAFLKE 120 I GAQ+ D+N SGAFTG+ S MLKEFG + ++GHSERR H ES E VA KFA +E Sbjct: 59 ITYGAQDCDVNTSGAFTGENSAVMLKEFGCKYTLVGHSERRVIHGESSEVVADKFAVAQE 118 Query: 121 NGLTPVLCIGESDAQNEAGETMAVCARQLDAVINTQGVEALEGAIIAYEPIWAIGTGKAA 180 NGL PVLCIGE+ Q EAGET AV QL AV+ G+ +L A+IAYEP+WAIGTGK A Sbjct: 119 NGLVPVLCIGETLEQFEAGETKAVVEAQLQAVVTKSGITSLNNAVIAYEPVWAIGTGKTA 178 Query: 181 TAEDAQRIHAQIRAHIAEKSEAVAKNVVIQYGGSVKPENAAAYFAQPDIDGALVGGAALD 240 T E AQ IHA IR+ +AE+ AVA V I YGGSVK N+A F Q DIDG LVGGA+LD Sbjct: 179 TPEIAQEIHAHIRSWLAEQDAAVANKVQILYGGSVKGANSAELFGQADIDGGLVGGASLD 238 Query: 241 AKSFAAIAKAAA 252 A F+ + A+ Sbjct: 239 AVEFSKVIAGAS 250 Lambda K H 0.314 0.130 0.364 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: 181 Number of extensions: 5 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: 256 Length of database: 251 Length adjustment: 24 Effective length of query: 232 Effective length of database: 227 Effective search space: 52664 Effective search space used: 52664 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: 41 (21.5 bits) S2: 47 (22.7 bits)
Align candidate WP_017222083.1 A923_RS0112890 (triose-phosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))
# 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/TIGR00419.hmm # target sequence database: /tmp/gapView.3595775.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00419 [M=228] Accession: TIGR00419 Description: tim: triose-phosphate isomerase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.5e-75 237.3 7.5 1.1e-74 237.1 7.5 1.0 1 NCBI__GCF_000276805.1:WP_017222083.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000276805.1:WP_017222083.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 237.1 7.5 1.1e-74 1.1e-74 1 227 [. 5 239 .. 5 240 .. 0.95 Alignments for each domain: == domain 1 score: 237.1 bits; conditional E-value: 1.1e-74 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 lv++n+Kln + +ve +++ l + ++a vevav pp v+++ v+ + i+ +Aq++d+++sGaftGe NCBI__GCF_000276805.1:WP_017222083.1 5 LVMGNWKLNATKASVEALINGLVDAAKDNATVEVAVCPPAVFIPQVEALTAdTAITYGAQDCDVNTSGAFTGE 77 79********************************************98665599******************* PP TIGR00419 73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnv 138 sA mlk++G+k++l+gHsErR ++ e++e+++ k+a+++e gl +v+C+getle+ e + ++++v NCBI__GCF_000276805.1:WP_017222083.1 78 NSAVMLKEFGCKYTLVGHSERRVIHGESSEVVADKFAVAQENGLVPVLCIGETLEQFEagetkavVEAQLQAV 150 **********************************************************666665555677777 PP TIGR00419 139 attaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaa 211 t+ ++ l+++v+A+EPv++iGtGk++++ a+++++ +r +l++ ++ va++v++lyG+sv++a++ael+ NCBI__GCF_000276805.1:WP_017222083.1 151 VTKSGITSLNNAVIAYEPVWAIGTGKTATPEIAQEIHAHIRSWLAEQDAAVANKVQILYGGSVKGANSAELFG 223 77777777***************************************************************** PP TIGR00419 212 qldvdGvLlasavlka 227 q d+dG L+++a+l a NCBI__GCF_000276805.1:WP_017222083.1 224 QADIDGGLVGGASLDA 239 *************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (251 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: 16.66 // [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