Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_012966597.1 FERP_RS10680 triose-phosphate isomerase
Query= BRENDA::Q58923 (219 letters) >NCBI__GCF_000025505.1:WP_012966597.1 Length = 222 Score = 272 bits (695), Expect = 4e-78 Identities = 133/215 (61%), Positives = 172/215 (80%) Query: 2 LIVINYKTYNESIGNRGLEIAKIAEKVSEESGITIGVAPQFVDLRMIVENVNIPVYAQHI 61 +++IN+K Y E G LE+AK EKV+E+S GVAP F+DL IV++V I VYAQH+ Sbjct: 5 VVIINFKAYREGAGKNALELAKAVEKVAEKSDFYFGVAPNFLDLAEIVKSVGIDVYAQHV 64 Query: 62 DNINPGSHTGHILAEAIKDCGCKGTLINHSEKRMLLADIEAVINKCKNLGLETIVCTNNI 121 D + GSHTG I AE IK+ G KG+LINHSE+R+ LADI+ +++K K LGL ++VCTNN+ Sbjct: 65 DAVEFGSHTGRITAEMIKEKGAKGSLINHSERRLRLADIDFLVSKFKELGLISVVCTNNV 124 Query: 122 NTSKAVAALSPDYIAVEPPELIGTGIPVSKANPEVVEGTVRAVKEINKDVKVLCGAGISK 181 +T+ A AALSPD++AVEPPELIG+GIPVSKA PEVVE +VRA K +N++VKVLCGAGI+K Sbjct: 125 STTAAAAALSPDFVAVEPPELIGSGIPVSKAEPEVVENSVRAAKNVNEEVKVLCGAGITK 184 Query: 182 GEDVKAALDLGAEGVLLASGVVKAKNVEEAIRELI 216 EDV AA+DLGA+GVLLASGVVKA + +A+ EL+ Sbjct: 185 YEDVVAAIDLGADGVLLASGVVKASDPRKALEELV 219 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: 202 Number of extensions: 4 Number of successful extensions: 1 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: 222 Length adjustment: 22 Effective length of query: 197 Effective length of database: 200 Effective search space: 39400 Effective search space used: 39400 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: 45 (21.9 bits)
Align candidate WP_012966597.1 FERP_RS10680 (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.4314.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-82 260.3 4.7 1e-81 260.1 4.7 1.0 1 lcl|NCBI__GCF_000025505.1:WP_012966597.1 FERP_RS10680 triose-phosphate is Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025505.1:WP_012966597.1 FERP_RS10680 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.1 4.7 1e-81 1e-81 1 227 [. 5 208 .. 5 209 .. 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 e+va++++ + +vap+f+dl +++ v i+v+Aq+vdav++G+ lcl|NCBI__GCF_000025505.1:WP_012966597.1 5 VVIINFKaYREGAGKNALELAKAVEKVAEKSDFYFGVAPNFLDLAEIVKSVG--IDVYAQHVDAVEFGS 71 69**************************************************..*************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137 +tG+i+Aem+k+ Gakg+li+HsErR l++ad i++ v++ kelgl svvC+ nn lcl|NCBI__GCF_000025505.1:WP_012966597.1 72 HTGRITAEMIKEKGAKGSLINHSERR--LRLAD--IDFLVSKFKELGLISVVCT-------------NN 123 **************************..*****..*******************.............** PP TIGR00419 138 vattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaed 206 v ttaaaaAl+pd+vAvEP+eliG+G+pvskAe+evve+svr ++k+v+e+v+vl+Ga++t+ ed lcl|NCBI__GCF_000025505.1:WP_012966597.1 124 VSTTAAAAALSPDFVAVEPPELIGSGIPVSKAEPEVVENSVR-----AAKNVNEEVKVLCGAGITKYED 187 ******************************************.....********************** PP TIGR00419 207 aelaaqldvdGvLlasavlka 227 + +a++l++dGvLlas+v+ka lcl|NCBI__GCF_000025505.1:WP_012966597.1 188 VVAAIDLGADGVLLASGVVKA 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.07 // [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