Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_002922909.1 KVAR_RS00455 triose-phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >NCBI__GCF_000025465.1:WP_002922909.1 Length = 255 Score = 471 bits (1212), Expect = e-138 Identities = 239/255 (93%), Positives = 246/255 (96%) Query: 1 MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60 MRHPLVMGNWKLNGSRHMV+ELV+NLR ELAGV+GCAVAIAPPEMY+D+AKR AEGSHI Sbjct: 1 MRHPLVMGNWKLNGSRHMVNELVANLRTELAGVSGCAVAIAPPEMYLDLAKRAAEGSHIH 60 Query: 61 LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120 LGAQNVD+NLSGAFTGETSA MLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG Sbjct: 61 LGAQNVDVNLSGAFTGETSAEMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120 Query: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP 180 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEG VIAYEPVWAIGTGKSATP Sbjct: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGVVIAYEPVWAIGTGKSATP 180 Query: 181 AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD 240 AQAQAVHKFIRDHIAK DA IAEQVIIQYGGSVNA NAAELF QPDIDGALVGGASLKAD Sbjct: 181 AQAQAVHKFIRDHIAKADAKIAEQVIIQYGGSVNAGNAAELFTQPDIDGALVGGASLKAD 240 Query: 241 AFAVIVKAAEAAKQA 255 AFAVIVKAAEAAK+A Sbjct: 241 AFAVIVKAAEAAKKA 255 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: 318 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: 255 Length adjustment: 24 Effective length of query: 231 Effective length of database: 231 Effective search space: 53361 Effective search space used: 53361 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 WP_002922909.1 KVAR_RS00455 (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.13456.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-110 353.6 3.7 3.1e-110 353.4 3.7 1.0 1 lcl|NCBI__GCF_000025465.1:WP_002922909.1 KVAR_RS00455 triose-phosphate is Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025465.1:WP_002922909.1 KVAR_RS00455 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 353.4 3.7 3.1e-110 3.1e-110 1 228 [] 5 240 .. 5 240 .. 1.00 Alignments for each domain: == domain 1 score: 353.4 bits; conditional E-value: 3.1e-110 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 lv++n+Kln+s+++v+++va+l+ e+a+++g++va+app+++ld +k+++e s+i+++Aqnvd++ sGa lcl|NCBI__GCF_000025465.1:WP_002922909.1 5 LVMGNWKLNGSRHMVNELVANLRTELAGVSGCAVAIAPPEMYLDLAKRAAEgSHIHLGAQNVDVNLSGA 73 79******************************************************************* PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere....... 130 ftGe+sAemlkd+Ga++++igHsErR+++ke+deli+kk+a+lke+gl++v+C+get++e+e lcl|NCBI__GCF_000025465.1:WP_002922909.1 74 FTGETSAEMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTPVLCIGETEAENEagkteev 142 ********************************************************************* PP TIGR00419 131 aartinnvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGa 199 +ar+i++v++t++aaA+e++v+A+EPv++iGtGk++++A+a++v+k++rdh++k+++++ae+v+++yG+ lcl|NCBI__GCF_000025465.1:WP_002922909.1 143 CARQIDAVLKTQGAAAFEGVVIAYEPVWAIGTGKSATPAQAQAVHKFIRDHIAKADAKIAEQVIIQYGG 211 ********************************************************************* PP TIGR00419 200 svtaaedaelaaqldvdGvLlasavlkae 228 sv+a+++ael+ q+d+dG+L+++a+lka+ lcl|NCBI__GCF_000025465.1:WP_002922909.1 212 SVNAGNAAELFTQPDIDGALVGGASLKAD 240 ***************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (255 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 6.29 // [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