Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_013684075.1 ARCVE_RS07030 triose-phosphate isomerase
Query= BRENDA::Q58923 (219 letters) >NCBI__GCF_000194625.1:WP_013684075.1 Length = 250 Score = 256 bits (655), Expect = 2e-73 Identities = 125/215 (58%), Positives = 166/215 (77%) Query: 2 LIVINYKTYNESIGNRGLEIAKIAEKVSEESGITIGVAPQFVDLRMIVENVNIPVYAQHI 61 +++IN+K Y E G + LE+AKIAE V+ I +AP +DL I+ V+I VYAQH+ Sbjct: 33 VVIINFKAYREGSGKQALELAKIAENVASRVDDYIAIAPPTIDLAEIINAVSIDVYAQHV 92 Query: 62 DNINPGSHTGHILAEAIKDCGCKGTLINHSEKRMLLADIEAVINKCKNLGLETIVCTNNI 121 D ++ GSHTG I AE +K+ G KG+LINHSE+R+ LADI+ +++K K LGL +IVCTNN+ Sbjct: 93 DAVDFGSHTGRITAEMVKEKGAKGSLINHSERRLRLADIDFLVSKFKELGLVSIVCTNNV 152 Query: 122 NTSKAVAALSPDYIAVEPPELIGTGIPVSKANPEVVEGTVRAVKEINKDVKVLCGAGISK 181 T+ A AAL+PDY+AVEPPELIG+GIPVSKA PE VE +V+A K++N +VKVLCGAGI + Sbjct: 153 ATTAAAAALNPDYVAVEPPELIGSGIPVSKAEPETVENSVKAAKDVNPNVKVLCGAGIGR 212 Query: 182 GEDVKAALDLGAEGVLLASGVVKAKNVEEAIRELI 216 ED ALDLGA+GVLLASG+VKAK+ + A+ EL+ Sbjct: 213 HEDYVTALDLGADGVLLASGIVKAKDPKAALEELV 247 Lambda K H 0.315 0.135 0.374 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: 223 Number of extensions: 11 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: 219 Length of database: 250 Length adjustment: 23 Effective length of query: 196 Effective length of database: 227 Effective search space: 44492 Effective search space used: 44492 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: 42 (22.0 bits) S2: 46 (22.3 bits)
Align candidate WP_013684075.1 ARCVE_RS07030 (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.9862.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-82 260.3 3.6 1e-81 260.1 3.6 1.0 1 lcl|NCBI__GCF_000194625.1:WP_013684075.1 ARCVE_RS07030 triose-phosphate i Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000194625.1:WP_013684075.1 ARCVE_RS07030 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.1 3.6 1e-81 1e-81 1 228 [] 33 237 .. 33 237 .. 0.99 Alignments for each domain: == domain 1 score: 260.1 bits; conditional E-value: 1e-81 TIGR00419 1 lviinfK.lnesvgkvelevaklaeevaseagvevavappfvdldvvkdeveseiqvaAqnvdavksGa 68 +viinfK ++e+ gk++le+ak+ae+vas+ + ++a+app +dl + ++v+ i+v+Aq+vdav++G+ lcl|NCBI__GCF_000194625.1:WP_013684075.1 33 VVIINFKaYREGSGKQALELAKIAENVASRVDDYIAIAPPTIDLAEIINAVS--IDVYAQHVDAVDFGS 99 69**************************************************..*************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137 +tG+i+Aem+k+ Gakg+li+HsErR l++ad i++ v++ kelgl s+vC+ nn lcl|NCBI__GCF_000194625.1:WP_013684075.1 100 HTGRITAEMVKEKGAKGSLINHSERR--LRLAD--IDFLVSKFKELGLVSIVCT-------------NN 151 **************************..*****..*******************.............** PP TIGR00419 138 vattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaed 206 vattaaaaAl+pd+vAvEP+eliG+G+pvskAe+e ve+sv+ ++k+v+++v+vl+Ga++ +ed lcl|NCBI__GCF_000194625.1:WP_013684075.1 152 VATTAAAAALNPDYVAVEPPELIGSGIPVSKAEPETVENSVK-----AAKDVNPNVKVLCGAGIGRHED 215 ******************************************.....********************** PP TIGR00419 207 aelaaqldvdGvLlasavlkae 228 + a++l++dGvLlas+++ka+ lcl|NCBI__GCF_000194625.1:WP_013684075.1 216 YVTALDLGADGVLLASGIVKAK 237 ********************96 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.52 // [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