Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_019613419.1 G327_RS0103720 triose-phosphate isomerase
Query= SwissProt::P50921 (256 letters) >NCBI__GCF_000381745.1:WP_019613419.1 Length = 250 Score = 263 bits (673), Expect = 2e-75 Identities = 136/251 (54%), Positives = 174/251 (69%), Gaps = 2/251 (0%) Query: 1 MRHPVVMGNWKLNGSKEMVVDLLNGLNAELEGVTGVDVAVAPPALFVDLAERTLTEAGSA 60 MR P+VMGNWKLNG+KE V L+ GL A + T V+VAV PPA+F++ LT A S Sbjct: 1 MRTPLVMGNWKLNGTKESVSTLIKGLEAAADAATNVEVAVCPPAIFIEQVAN-LTAANS- 58 Query: 61 IILGAQNTDLNNSGAFTGDMSPAMLKEFGATHIIIGHSERREYHAESDEFVAKKFAFLKE 120 I GAQ+ N GA+TG+ SP M+KEFGA + ++GHSERR+YH E+D VA KF +++ Sbjct: 59 IEFGAQDVSTNVEGAYTGETSPVMVKEFGAKYSLVGHSERRQYHNETDAVVAAKFVAIQK 118 Query: 121 NGLTPVLCIGESDAQNEAGETMAVCARQLDAVINTQGVEALEGAIIAYEPIWAIGTGKAA 180 +GL PVLCIGE+ + E T V QL AVI+ G++ALE +IAYEP+WAIGTGK A Sbjct: 119 HGLVPVLCIGETLEERETNVTTTVVETQLKAVIDLAGIDALENCVIAYEPVWAIGTGKVA 178 Query: 181 TAEDAQRIHAQIRAHIAEKSEAVAKNVVIQYGGSVKPENAAAYFAQPDIDGALVGGAALD 240 T+E AQ +HA IR+ +AE+S+ VA+ V I YGGSVK +A FAQ DIDG LVGGAAL Sbjct: 179 TSEQAQEVHAHIRSWLAEQSKVVAEKVQILYGGSVKAASAKELFAQADIDGGLVGGAALI 238 Query: 241 AKSFAAIAKAA 251 + F I + A Sbjct: 239 IEEFVGIIEGA 249 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: 3 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: 250 Length adjustment: 24 Effective length of query: 232 Effective length of database: 226 Effective search space: 52432 Effective search space used: 52432 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: 46 (22.3 bits)
Align candidate WP_019613419.1 G327_RS0103720 (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.1910531.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-72 230.2 9.6 1.6e-72 230.1 9.6 1.0 1 NCBI__GCF_000381745.1:WP_019613419.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000381745.1:WP_019613419.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 230.1 9.6 1.6e-72 1.6e-72 1 225 [. 5 237 .. 5 240 .. 0.93 Alignments for each domain: == domain 1 score: 230.1 bits; conditional E-value: 1.6e-72 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 lv++n+Kln++ ++v +++ l++ ++vevav pp ++++ v++ + i+ +Aq+v ++ Ga+tGe NCBI__GCF_000381745.1:WP_019613419.1 5 LVMGNWKLNGTKESVSTLIKGLEAAADAATNVEVAVCPPAIFIEQVANLTAaNSIEFGAQDVSTNVEGAYTGE 77 79***********************999******************99766589******************* PP TIGR00419 73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaa 145 +s m+k++Gak++l+gHsErR +++e+d ++++k+ +++ gl +v+C+getleere+ t +v t+ +a+ NCBI__GCF_000381745.1:WP_019613419.1 78 TSPVMVKEFGAKYSLVGHSERRQYHNETDAVVAAKFVAIQKHGLVPVLCIGETLEERETNVTTTVVETQLKAV 150 **********************************************************555555555555554 PP TIGR00419 146 A.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaa 211 le+ v+A+EPv++iGtGk+++ +a++v++ +r +l++ sk vae+v++lyG+sv+aa+++el+a NCBI__GCF_000381745.1:WP_019613419.1 151 IdlagidaLENCVIAYEPVWAIGTGKVATSEQAQEVHAHIRSWLAEQSKVVAEKVQILYGGSVKAASAKELFA 223 34444444***************************************************************** PP TIGR00419 212 qldvdGvLlasavl 225 q d+dG L+++a l NCBI__GCF_000381745.1:WP_019613419.1 224 QADIDGGLVGGAAL 237 ***********987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (250 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: 15.25 // [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