Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_011024480.1 MA_RS24040 triose-phosphate isomerase
Query= BRENDA::Q12UK2 (221 letters) >NCBI__GCF_000007345.1:WP_011024480.1 Length = 222 Score = 336 bits (861), Expect = 2e-97 Identities = 168/219 (76%), Positives = 193/219 (88%) Query: 3 PLIVLNLKTYLEGTGEGAVRIARACKEVGEASGIEIAIAPQFCDIYRVASQVDVPVYSQH 62 P I+LN KTY +GTG+GAV IARAC+ V E SGIEIA+APQ DIYRVAS+V++P++SQH Sbjct: 4 PFILLNYKTYNQGTGQGAVEIARACRAVSEESGIEIAVAPQLPDIYRVASEVELPIFSQH 63 Query: 63 LDGVGAGSFTGHAFAKCIKDAGAVGTLINHSECRLKLADIEASVTAAKGEGLRTIICTNN 122 +DGVGAGSFTGH F KCIK+AGAVGTLINHSE RL LA+IEAS+ AAK GLR +ICTNN Sbjct: 64 MDGVGAGSFTGHVFGKCIKEAGAVGTLINHSERRLTLAEIEASLKAAKEFGLRAVICTNN 123 Query: 123 IATTAAAAALGPDYVAVEPPELIGSGIPVSKADPEVVTGSVAAVERIDPAVKVLCGAGIS 182 + TTAAAAAL PDYVA+EPPELIGSGIPVSKADPEVV+GSV AV +I+ VKVLCGAGIS Sbjct: 124 VPTTAAAAALEPDYVAIEPPELIGSGIPVSKADPEVVSGSVEAVAKINSGVKVLCGAGIS 183 Query: 183 KGEDLKAAIELGSVGVLLASGIVKAKDPKAALEDLVSLI 221 KGEDL+AA++LGS GVLLASGIVKA DPKAALEDL+ L+ Sbjct: 184 KGEDLRAALDLGSQGVLLASGIVKAADPKAALEDLIRLV 222 Lambda K H 0.316 0.134 0.378 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: 270 Number of extensions: 13 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: 221 Length of database: 222 Length adjustment: 22 Effective length of query: 199 Effective length of database: 200 Effective search space: 39800 Effective search space used: 39800 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 (21.6 bits) S2: 45 (21.9 bits)
Align candidate WP_011024480.1 MA_RS24040 (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.aa/TIGR00419.hmm # target sequence database: /tmp/gapView.27569.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-70 222.2 1.8 4.8e-70 221.9 1.8 1.0 1 lcl|NCBI__GCF_000007345.1:WP_011024480.1 MA_RS24040 triose-phosphate isom Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007345.1:WP_011024480.1 MA_RS24040 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 221.9 1.8 4.8e-70 4.8e-70 1 227 [. 5 208 .. 5 209 .. 0.99 Alignments for each domain: == domain 1 score: 221.9 bits; conditional E-value: 4.8e-70 TIGR00419 1 lviinfK.lnesvgkvelevaklaeevaseagvevavappfvdldvvkdeveseiqvaAqnvdavksGa 68 ++++n+K +n+++g+ + e+a+ ++ v++e+g+e+avap+ d+ +v+ eve +++ q++d v +G+ lcl|NCBI__GCF_000007345.1:WP_011024480.1 5 FILLNYKtYNQGTGQGAVEIARACRAVSEESGIEIAVAPQLPDIYRVASEVE--LPIFSQHMDGVGAGS 71 6899************************************************..*************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137 ftG++ +++k++Ga g+li+HsErR l +a+ ie+ + +ke gl++v+C+ nn lcl|NCBI__GCF_000007345.1:WP_011024480.1 72 FTGHVFGKCIKEAGAVGTLINHSERR--LTLAE--IEASLKAAKEFGLRAVICT-------------NN 123 **************************..*****..*******************.............** PP TIGR00419 138 vattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaed 206 v ttaaaaAlepd+vA+EP+eliG+G+pvskA++evv +sv+ ++++++ v+vl+Ga+++++ed lcl|NCBI__GCF_000007345.1:WP_011024480.1 124 VPTTAAAAALEPDYVAIEPPELIGSGIPVSKADPEVVSGSVE-----AVAKINSGVKVLCGAGISKGED 187 ******************************************.....********************** PP TIGR00419 207 aelaaqldvdGvLlasavlka 227 ++a++l+ +GvLlas+++ka lcl|NCBI__GCF_000007345.1:WP_011024480.1 188 LRAALDLGSQGVLLASGIVKA 208 ********************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (222 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: 00:00:00.00 # Mc/sec: 9.02 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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