Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_019864233.1 METMI_RS0100685 triose-phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >NCBI__GCF_000384075.1:WP_019864233.1 Length = 249 Score = 233 bits (595), Expect = 2e-66 Identities = 122/249 (48%), Positives = 164/249 (65%), Gaps = 9/249 (3%) Query: 1 MRHPLVMGNWKLNGSR----HMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEG 56 MR LV+GNWK+NG+R + +++ L + AG+A CA P +++ +G Sbjct: 1 MRQSLVIGNWKMNGTRASADSLAQGILAGLGENTAGIAVCA-----PYVFLPNVSEITKG 55 Query: 57 SHIMLGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVL 116 S + LGAQNV SGA+TGE SA+ML + G Y ++GHSERR+Y+ ++D +A +F Sbjct: 56 SRLALGAQNVADQASGAYTGEVSASMLSEFGCTYALVGHSERRSYYGDTDASVAARFCQA 115 Query: 117 KEQGLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGK 176 + Q + PVLCIGET E E +T V +Q+DAV+ G AAF AVIAYEPVWAIGTGK Sbjct: 116 QAQNIIPVLCIGETLEEREQEQTFAVVEKQLDAVIGLAGIAAFANAVIAYEPVWAIGTGK 175 Query: 177 SATPAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGAS 236 +A+ AQAQ VH+ IR++IA D IA+++ I YGGS NA LFA PDIDG L+GGAS Sbjct: 176 TASDAQAQEVHQHIREYIAAKDQTIADKIQILYGGSAKPDNAKGLFAMPDIDGGLIGGAS 235 Query: 237 LKADAFAVI 245 L A++F I Sbjct: 236 LDAESFLKI 244 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: 185 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: 255 Length of database: 249 Length adjustment: 24 Effective length of query: 231 Effective length of database: 225 Effective search space: 51975 Effective search space used: 51975 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: 46 (22.3 bits)
Align candidate WP_019864233.1 METMI_RS0100685 (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.6964.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-71 225.4 1.1 4.8e-71 225.2 1.1 1.0 1 lcl|NCBI__GCF_000384075.1:WP_019864233.1 METMI_RS0100685 triose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384075.1:WP_019864233.1 METMI_RS0100685 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 225.2 1.1 4.8e-71 4.8e-71 1 228 [] 5 239 .. 5 239 .. 0.97 Alignments for each domain: == domain 1 score: 225.2 bits; conditional E-value: 4.8e-71 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 lvi+n+K+n+++ + + + + + + + +++ +av p+v+l+ v++ + s++ ++Aqnv + sGa lcl|NCBI__GCF_000384075.1:WP_019864233.1 5 LVIGNWKMNGTRASADSLAQGILAGLGENT-AGIAVCAPYVFLPNVSEITKgSRLALGAQNVADQASGA 72 79**********************998765.6899*************9999***************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere....... 130 +tGe+sA ml ++G+ + l+gHsErRs+ +d +++++ +++++++ +v+C+getleere lcl|NCBI__GCF_000384075.1:WP_019864233.1 73 YTGEVSASMLSEFGCTYALVGHSERRSYYGDTDASVAARFCQAQAQNIIPVLCIGETLEEREqeqtfav 141 **************************************************************9999998 PP TIGR00419 131 aartinnvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGa 199 + +++++v a++aA+ ++v+A+EPv++iGtGk++s A+a++v++ +r++++ ++ +a+++++lyG+ lcl|NCBI__GCF_000384075.1:WP_019864233.1 142 VEKQLDAVIGLAGIAAFANAVIAYEPVWAIGTGKTASDAQAQEVHQHIREYIAAKDQTIADKIQILYGG 210 8999***************************************************************** PP TIGR00419 200 svtaaedaelaaqldvdGvLlasavlkae 228 s + +++ l+a +d+dG L+++a+l ae lcl|NCBI__GCF_000384075.1:WP_019864233.1 211 SAKPDNAKGLFAMPDIDGGLIGGASLDAE 239 **************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (249 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: 5.79 // [ok]
This GapMind analysis is from Sep 24 2021. 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