Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_011305955.1 MBAR_RS05035 triose-phosphate isomerase
Query= BRENDA::Q12UK2 (221 letters) >NCBI__GCF_000195895.1:WP_011305955.1 Length = 222 Score = 343 bits (879), Expect = 2e-99 Identities = 172/219 (78%), Positives = 195/219 (89%) Query: 3 PLIVLNLKTYLEGTGEGAVRIARACKEVGEASGIEIAIAPQFCDIYRVASQVDVPVYSQH 62 P IVLN KTYL+GTG+GA+ IA+ACK V E SG+EIA+APQ DIYRVAS+V +PV+SQH Sbjct: 4 PFIVLNYKTYLQGTGQGAMEIAKACKAVSEESGVEIAVAPQLPDIYRVASEVALPVFSQH 63 Query: 63 LDGVGAGSFTGHAFAKCIKDAGAVGTLINHSECRLKLADIEASVTAAKGEGLRTIICTNN 122 LDG+GAGSFTGH F KCIK+AGAVGTLINHSE RL LA+IEAS+ AAK GLR+IICTNN Sbjct: 64 LDGIGAGSFTGHVFGKCIKEAGAVGTLINHSEKRLTLAEIEASLKAAKEFGLRSIICTNN 123 Query: 123 IATTAAAAALGPDYVAVEPPELIGSGIPVSKADPEVVTGSVAAVERIDPAVKVLCGAGIS 182 + TTAAAA LGPDYVA+EPPELIGSGIPVSKADPEVV+GSV AV +I+P VKVLCGAGIS Sbjct: 124 VPTTAAAAVLGPDYVAIEPPELIGSGIPVSKADPEVVSGSVEAVAKINPRVKVLCGAGIS 183 Query: 183 KGEDLKAAIELGSVGVLLASGIVKAKDPKAALEDLVSLI 221 KGEDL+AA++LGS GVLLASGIVKA DPKAALEDL+ LI Sbjct: 184 KGEDLRAALDLGSQGVLLASGIVKATDPKAALEDLIRLI 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: 258 Number of extensions: 12 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_011305955.1 MBAR_RS05035 (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.7631.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-69 219.5 1.5 3.1e-69 219.3 1.5 1.0 1 lcl|NCBI__GCF_000195895.1:WP_011305955.1 MBAR_RS05035 triose-phosphate is Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195895.1:WP_011305955.1 MBAR_RS05035 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 219.3 1.5 3.1e-69 3.1e-69 1 227 [. 5 208 .. 5 209 .. 0.99 Alignments for each domain: == domain 1 score: 219.3 bits; conditional E-value: 3.1e-69 TIGR00419 1 lviinfK.lnesvgkvelevaklaeevaseagvevavappfvdldvvkdeveseiqvaAqnvdavksGa 68 ++++n+K + +++g+ ++e+ak ++ v++e+gve+avap+ d+ +v+ ev ++v q++d + +G+ lcl|NCBI__GCF_000195895.1:WP_011305955.1 5 FIVLNYKtYLQGTGQGAMEIAKACKAVSEESGVEIAVAPQLPDIYRVASEVA--LPVFSQHLDGIGAGS 71 699*************************************************..*************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137 ftG++ +++k++Ga g+li+HsE+R l +a+ ie+ + +ke gl+s++C+ nn lcl|NCBI__GCF_000195895.1:WP_011305955.1 72 FTGHVFGKCIKEAGAVGTLINHSEKR--LTLAE--IEASLKAAKEFGLRSIICT-------------NN 123 **************************..*****..*******************.............** PP TIGR00419 138 vattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaed 206 v ttaaaa l pd+vA+EP+eliG+G+pvskA++evv +sv+ +++++++ v+vl+Ga+++++ed lcl|NCBI__GCF_000195895.1:WP_011305955.1 124 VPTTAAAAVLGPDYVAIEPPELIGSGIPVSKADPEVVSGSVE-----AVAKINPRVKVLCGAGISKGED 187 ******************************************.....********************** PP TIGR00419 207 aelaaqldvdGvLlasavlka 227 ++a++l+ +GvLlas+++ka lcl|NCBI__GCF_000195895.1:WP_011305955.1 188 LRAALDLGSQGVLLASGIVKA 208 ********************9 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 5.81 // [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