Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate GFF3129 HP15_3071 triosephosphate isomerase
Query= BRENDA::P0A858 (255 letters) >FitnessBrowser__Marino:GFF3129 Length = 252 Score = 218 bits (556), Expect = 7e-62 Identities = 119/252 (47%), Positives = 160/252 (63%), Gaps = 3/252 (1%) Query: 1 MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVA-GCAVAIAPPEMYIDMAKREAEGSHI 59 MR +V GNWK+NGS+ + LVS++R + A + G V I PP +Y+ A G + Sbjct: 1 MRRKIVAGNWKMNGSKDLAQTLVSDVRSQAASLDNGVEVVIIPPAIYVPDVVASA-GDVL 59 Query: 60 MLGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQ 119 +G QNV SGA+TGE SA M D G QY ++GHSERR E+D +A+K + Sbjct: 60 SVGVQNVAQWASGAYTGEISADMALDQGCQYALVGHSERRQLFAETDAAVAEKVGRILAS 119 Query: 120 GLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSAT 179 GL ++C+GET E EAGK E V A Q+ A L T + ++ V+AYEPVWAIGTGK+AT Sbjct: 120 GLQAMVCVGETLEEREAGKAETVVAAQVKAGLATVASEQWQRVVVAYEPVWAIGTGKTAT 179 Query: 180 PAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKA 239 AQA+H IR ++++ A A ++ + YGGSV A NAA LFA+PDIDG L+GGASLKA Sbjct: 180 AQDAQAMHASIRQVLSEMGAP-ANEISLLYGGSVKADNAAALFAEPDIDGGLIGGASLKA 238 Query: 240 DAFAVIVKAAEA 251 + F I ++ A Sbjct: 239 EDFVSICRSVPA 250 Lambda K H 0.316 0.130 0.366 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: 158 Number of extensions: 7 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: 255 Length of database: 252 Length adjustment: 24 Effective length of query: 231 Effective length of database: 228 Effective search space: 52668 Effective search space used: 52668 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: 47 (22.7 bits)
Align candidate GFF3129 HP15_3071 (triosephosphate 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.1068733.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-67 212.7 7.3 3.7e-67 212.5 7.3 1.0 1 FitnessBrowser__Marino:GFF3129 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Marino:GFF3129 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 212.5 7.3 3.7e-67 3.7e-67 1 228 [] 5 239 .. 5 239 .. 0.94 Alignments for each domain: == domain 1 score: 212.5 bits; conditional E-value: 3.7e-67 TIGR00419 1 lviinfKlnesvgkvelevaklaeevas.eagvevavappfvdldvvkdeveseiqvaAqnvdavksGaftGeisAeml 78 +v +n+K+n+s +++v++++ + as +gvev++ pp ++++ v+ + ++v+ qnv sGa+tGeisA+m+ FitnessBrowser__Marino:GFF3129 5 IVAGNWKMNGSKDLAQTLVSDVRSQAASlDNGVEVVIIPPAIYVPDVVASAGDVLSVGVQNVAQWASGAYTGEISADMA 83 699*********************99983569********************9************************** PP TIGR00419 79 kdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaa.aA......lepd 150 d G+++ l+gHsErR l++e+d +++kv r+ + gl+++vCvgetleerea++ +va + +a A ++ + FitnessBrowser__Marino:GFF3129 84 LDQGCQYALVGHSERRQLFAETDAAVAEKVGRILASGLQAMVCVGETLEEREAGKAETVVAAQVKAgLAtvaseqWQRV 162 ****************************************************99999999888766233677999**** PP TIGR00419 151 vvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdGvLlasavlkae 228 vvA+EPv++iGtGk+++ +a+++++s+r+ l++ + a+++++lyG+sv+a ++a l+a++d+dG L+++a+lkae FitnessBrowser__Marino:GFF3129 163 VVAYEPVWAIGTGKTATAQDAQAMHASIRQVLSEMGAP-ANEISLLYGGSVKADNAAALFAEPDIDGGLIGGASLKAE 239 *****************************888876665.6789*********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (252 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 14.65 // [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