Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_013645965.1 METBO_RS11890 triose-phosphate isomerase
Query= SwissProt::O74025 (226 letters) >NCBI__GCF_000191585.1:WP_013645965.1 Length = 226 Score = 333 bits (853), Expect = 2e-96 Identities = 167/226 (73%), Positives = 196/226 (86%) Query: 1 MNEIKETPIVILNFKTYLESTGENALKLAKGSEMVAEETGVNIMVHPQYADIYRIAHEVN 60 MN K TPIVILNFKTYLESTG NA+ LA SEMVAEETG+N++V PQ +DIY+++++VN Sbjct: 1 MNNTKRTPIVILNFKTYLESTGINAVNLATASEMVAEETGINMVVAPQSSDIYQLSNKVN 60 Query: 61 IPVLAQHIDTIDAGGHTGSILPECVKEAGAVGTLINHSERRVELFEIDAAIKKADSLGLS 120 IPV AQHID +DAGGHTGS L ECVKEAGA G+LINHSE+R++L +ID A+KK + Sbjct: 61 IPVFAQHIDAVDAGGHTGSTLIECVKEAGADGSLINHSEQRMKLADIDVAVKKLAQKNMV 120 Query: 121 TVVCTNNIETSSAAATLNPDFVAIEPPELIGSGIPVSKPEPEIVEKTVESIHNINPEVRV 180 +V+CTNNIETS+A ATL PDFVAIEPPELIGSGIPVSK EPEIVE TVE IH I+PE+ V Sbjct: 121 SVLCTNNIETSAAVATLKPDFVAIEPPELIGSGIPVSKAEPEIVEGTVEVIHKIDPEISV 180 Query: 181 LCGAGISTGDDLKAAIDLGSEGVLLASGIILADDPKKALLDLVSKI 226 LCGAGISTGDD+KAA+DLG++GVLLASGII ADDPK+ALL+LVSKI Sbjct: 181 LCGAGISTGDDMKAAMDLGADGVLLASGIIKADDPKEALLNLVSKI 226 Lambda K H 0.313 0.133 0.368 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: 243 Number of extensions: 7 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: 226 Length of database: 226 Length adjustment: 22 Effective length of query: 204 Effective length of database: 204 Effective search space: 41616 Effective search space used: 41616 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 46 (22.3 bits)
Align candidate WP_013645965.1 METBO_RS11890 (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.3369243.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-70 223.5 6.2 1.9e-70 223.3 6.2 1.0 1 NCBI__GCF_000191585.1:WP_013645965.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000191585.1:WP_013645965.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 223.3 6.2 1.9e-70 1.9e-70 1 228 [] 9 213 .. 9 213 .. 0.99 Alignments for each domain: == domain 1 score: 223.3 bits; conditional E-value: 1.9e-70 TIGR00419 1 lviinfK.lnesvgkvelevaklaeevaseagvevavappfvdldvvkdeveseiqvaAqnvdavksGaftGe 72 +vi+nfK + es+g + +a+ +e va+e+g++++vap+ d+ ++++v+ i+v Aq++dav++G++tG+ NCBI__GCF_000191585.1:WP_013645965.1 9 IVILNFKtYLESTGINAVNLATASEMVAEETGINMVVAPQSSDIYQLSNKVN--IPVFAQHIDAVDAGGHTGS 79 79**************************************************..******************* PP TIGR00419 73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaa 145 ++ e++k++Ga g+li+HsE+R +k+ad i+ v +l ++++ sv+C+ nn+ t+aa+a NCBI__GCF_000191585.1:WP_013645965.1 80 TLIECVKEAGADGSLINHSEQR--MKLAD--IDVAVKKLAQKNMVSVLCT-------------NNIETSAAVA 135 **********************..*****..*******************.............********** PP TIGR00419 146 AlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdGv 218 l+pd+vA+EP+eliG+G+pvskAe+e ve++v+ v +++ ++++vl+Ga++++++d+++a++l++dGv NCBI__GCF_000191585.1:WP_013645965.1 136 TLKPDFVAIEPPELIGSGIPVSKAEPEIVEGTVE-----VIHKIDPEISVLCGAGISTGDDMKAAMDLGADGV 203 **********************************.....99******************************** PP TIGR00419 219 Llasavlkae 228 Llas+++ka+ NCBI__GCF_000191585.1:WP_013645965.1 204 LLASGIIKAD 213 ********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (226 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: 14.03 // [ok]
This GapMind analysis is from Apr 09 2024. 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