Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_093429068.1 BM272_RS12175 triose-phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >NCBI__GCF_900112605.1:WP_093429068.1 Length = 250 Score = 255 bits (651), Expect = 7e-73 Identities = 129/249 (51%), Positives = 164/249 (65%) Query: 1 MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60 MR PLV GNWK+NG R L++ ++ + V VA+ P +Y+ +R+ E S I Sbjct: 1 MRQPLVAGNWKMNGDRATNEALLNGIKAGIGDVEQSEVAVCAPFVYLADVQRQLEASPIR 60 Query: 61 LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120 G+Q+V GAFTGE S MLKD G Y I+GHSERR+ H E ++ +A+KFA +E G Sbjct: 61 WGSQDVSAEPKGAFTGEVSVTMLKDFGCHYAIVGHSERRSLHGEDNDTVARKFAAAREGG 120 Query: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP 180 + P+LC+GET AE EA TE+V Q+DAV+ G AA VIAYEPVWAIGTG +ATP Sbjct: 121 IRPILCVGETLAEREADTTEQVVGAQLDAVMDAVGPAALADGVIAYEPVWAIGTGHTATP 180 Query: 181 AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD 240 QAQA+H FIR +A DA A+ + I YGGS+ +NAAEL AQ DIDG L+GGASL AD Sbjct: 181 EQAQAMHAFIRQRVADRDAATADALRILYGGSMKGANAAELMAQSDIDGGLIGGASLDAD 240 Query: 241 AFAVIVKAA 249 F I +AA Sbjct: 241 EFLTICRAA 249 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: 188 Number of extensions: 6 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: 255 Length of database: 250 Length adjustment: 24 Effective length of query: 231 Effective length of database: 226 Effective search space: 52206 Effective search space used: 52206 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_093429068.1 BM272_RS12175 (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.3742760.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-71 227.3 0.4 1.2e-71 227.1 0.4 1.0 1 NCBI__GCF_900112605.1:WP_093429068.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900112605.1:WP_093429068.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 227.1 0.4 1.2e-71 1.2e-71 1 228 [] 5 240 .. 5 240 .. 0.99 Alignments for each domain: == domain 1 score: 227.1 bits; conditional E-value: 1.2e-71 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 lv +n+K+n+ + + e +++ +++ + ++++ evav pfv+l v++++e s i+ + q+v a +GaftGe NCBI__GCF_900112605.1:WP_093429068.1 5 LVAGNWKMNGDRATNEALLNGIKAGIGDVEQSEVAVCAPFVYLADVQRQLEaSPIRWGSQDVSAEPKGAFTGE 77 799************************************************999******************* PP TIGR00419 73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnv 138 +s mlkd+G+++ ++gHsErRsl+ e ++ ++ k+a ++e g+++++Cvgetl+ere ++ ++++v NCBI__GCF_900112605.1:WP_093429068.1 78 VSVTMLKDFGCHYAIVGHSERRSLHGEDNDTVARKFAAAREGGIRPILCVGETLAEREadtteqvVGAQLDAV 150 **********************************************************99999999******* PP TIGR00419 139 attaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaa 211 ++ + aAl + v+A+EPv++iGtG ++++ +a+++++++r+ ++ ++ a+ r+lyG+s+++a++ael+a NCBI__GCF_900112605.1:WP_093429068.1 151 MDAVGPAALADGVIAYEPVWAIGTGHTATPEQAQAMHAFIRQRVADRDAATADALRILYGGSMKGANAAELMA 223 ************************************************************************* PP TIGR00419 212 qldvdGvLlasavlkae 228 q d+dG L+++a+l a+ NCBI__GCF_900112605.1:WP_093429068.1 224 QSDIDGGLIGGASLDAD 240 **************987 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 20.10 // [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