Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_089214123.1 CHB69_RS00990 triose-phosphate isomerase
Query= SwissProt::Q8L1Z5 (254 letters) >NCBI__GCF_900188185.1:WP_089214123.1 Length = 247 Score = 202 bits (513), Expect = 7e-57 Identities = 111/244 (45%), Positives = 145/244 (59%), Gaps = 6/244 (2%) Query: 6 RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENILL 65 R ++ GNWKMNG +L E AI AG + + +C P TL+ LGG Sbjct: 4 RKYVVGNWKMNGLSGALAEAEAIFAGARAH--EAVDVALCPPFTLIG-PMAALGGAT--- 57 Query: 66 GGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAGL 125 GGQ+CH G +TG +SA ML +AGA+ VI+GHSERR + E DA V+AK AA AGL Sbjct: 58 GGQDCHPQPSGAFTGSVSAPMLADAGAALVIVGHSERREGFAERDADVKAKAGAALTAGL 117 Query: 126 VALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSADV 185 ++CVGE L R+S +D + Q++GSLP + +AYEP+WA+GTG T DV Sbjct: 118 SVILCVGEPLGVRESGGAIDYVLAQVQGSLPGDFDPARLAVAYEPIWAIGTGRVPTIEDV 177 Query: 186 AEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAIDFL 245 A +H I + R G+ A +RLLYGGSV NA +LL V+GAL+GGASL A FL Sbjct: 178 AAMHGAIRAALSDRIGEGAAAVRLLYGGSVNGDNAADLLGARDVDGALVGGASLTAAKFL 237 Query: 246 TICD 249 I + Sbjct: 238 PIVE 241 Lambda K H 0.320 0.137 0.403 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: 241 Number of extensions: 11 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: 254 Length of database: 247 Length adjustment: 24 Effective length of query: 230 Effective length of database: 223 Effective search space: 51290 Effective search space used: 51290 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: 46 (22.3 bits)
Align candidate WP_089214123.1 CHB69_RS00990 (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.1979331.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-45 140.4 0.1 4.9e-45 140.1 0.1 1.0 1 NCBI__GCF_900188185.1:WP_089214123.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900188185.1:WP_089214123.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 140.1 0.1 4.9e-45 4.9e-45 2 227 .. 7 233 .. 6 234 .. 0.91 Alignments for each domain: == domain 1 score: 140.1 bits; conditional E-value: 4.9e-45 TIGR00419 2 viinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeveseiqvaAqnvdavksGaftGeis 74 v++n+K+n+ g ++ a a a+ + v va+ ppf + ++ + q+++ + sGaftG++s NCBI__GCF_900188185.1:WP_089214123.1 7 VVGNWKMNGLSGALAEAEAIFAGARAH-EAVDVALCPPFTLIGPMAALGG---ATGGQDCHPQPSGAFTGSVS 75 89*******999998877766666665.5689*******99977665544...789***************** PP TIGR00419 75 AemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaaA. 146 A ml+d+Ga+ v++gHsErR ++e d +++k + gl +++Cvge l re++ i+ v+ + + NCBI__GCF_900188185.1:WP_089214123.1 76 APMLADAGAALVIVGHSERREGFAERDADVKAKAGAALTAGLSVILCVGEPLGVRESGGAIDYVLAQVQGSLp 148 ***********************999999***********************************988776655 PP TIGR00419 147 ..lepd..vvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldv 215 ++p+ vA+EP+++iGtG++ + + ++++ +r l+ e a vr+lyG+sv++ ++a+l dv NCBI__GCF_900188185.1:WP_089214123.1 149 gdFDPArlAVAYEPIWAIGTGRVPTIEDVAAMHGAIRAALSDRIGEGAAAVRLLYGGSVNGDNAADLLGARDV 221 78887643699**************************9999999999************************** PP TIGR00419 216 dGvLlasavlka 227 dG+L+++a+l a NCBI__GCF_900188185.1:WP_089214123.1 222 DGALVGGASLTA 233 *********987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (247 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: 20.58 // [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