Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate Ac3H11_1454 Triosephosphate isomerase (EC 5.3.1.1)
Query= BRENDA::Q10657 (247 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1454 Length = 249 Score = 223 bits (568), Expect = 3e-63 Identities = 128/247 (51%), Positives = 166/247 (67%), Gaps = 7/247 (2%) Query: 3 RKFFVGGNWKMNGDYASVDGIVTFLNASADNSSVDVVVAPPAPYLAYAKSKLKAG--VLV 60 +K + GNWKMNG A+ + ++ L A + + DV VA PAPYLA ++ L AG V V Sbjct: 4 KKKLIAGNWKMNGSLAANEVLLKALIAGLGDVTCDVAVAVPAPYLAQVQA-LTAGTAVAV 62 Query: 61 AAQNCYKVPKGAFTGEISPAMIKDLGLEWVILGHSERRHVFGESDALIAEKTVHALEAGI 120 AAQ+ + GA+TGE+S AM+KD G+ + ++GHSERR GE+D +AEK AL AG+ Sbjct: 63 AAQDVSRYESGAYTGEVSVAMLKDFGVRYALVGHSERRQYHGETDVAVAEKAQRALAAGV 122 Query: 121 KVVFCIGEKLEEREAGHTKDVNFRQLQAIVD-KGVSWENIVIAYEPVWAIGTGKTASGEQ 179 + C+GE LEEREAG T+ V RQL A++ G IV+AYEPVWAIGTG+TAS EQ Sbjct: 123 TPIVCVGETLEEREAGQTEAVVKRQLAAVIHLNGHCISEIVVAYEPVWAIGTGRTASPEQ 182 Query: 180 AQEVHEWIRAFLKEKVSPAVADATRIIYGGSVTADNAAELGKKPDIDGFLVGGASLK-PD 238 AQ VH +RA L + AD R++YGGS+ A NAA+L +PDIDG LVGGASLK D Sbjct: 183 AQAVHAVLRAQL--AAASEHADRIRLLYGGSMNAGNAAQLLAQPDIDGGLVGGASLKAAD 240 Query: 239 FVKIINA 245 F++II A Sbjct: 241 FLQIIAA 247 Lambda K H 0.317 0.134 0.396 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: 187 Number of extensions: 11 Number of successful extensions: 4 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: 247 Length of database: 249 Length adjustment: 24 Effective length of query: 223 Effective length of database: 225 Effective search space: 50175 Effective search space used: 50175 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 Ac3H11_1454 (Triosephosphate isomerase (EC 5.3.1.1))
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.3830.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-67 211.6 6.4 7.8e-67 211.4 6.4 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1454 Triosephosphate isomerase (EC 5. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1454 Triosephosphate isomerase (EC 5.3.1.1) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 211.4 6.4 7.8e-67 7.8e-67 1 227 [. 7 238 .. 7 239 .. 0.94 Alignments for each domain: == domain 1 score: 211.4 bits; conditional E-value: 7.8e-67 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnv 61 l+ +n+K+n+s+ e ++ l + + ++ + vava+p +l v+ + + vaAq+v lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1454 7 LIAGNWKMNGSLAANEVLLKALIAGLGDV-TCDVAVAVPAPYLAQVQALTAgTAVAVAAQDV 67 689**********************9987.599999999999999998777799******** PP TIGR00419 62 davksGaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvg 123 +sGa+tGe+s +mlkd+G+++ l+gHsErR ++ e+d +++k r+ + g++++vCvg lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1454 68 SRYESGAYTGEVSVAMLKDFGVRYALVGHSERRQYHGETDVAVAEKAQRALAAGVTPIVCVG 129 ************************************************************** PP TIGR00419 124 etleereaartinnvattaaaaA......lepdvvAvEPveliGtGkpvskAeaevveksvr 179 etleerea++t +v+++ aa+ +++ vvA+EPv++iGtG+++s+ +a++v++ +r lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1454 130 ETLEEREAGQTEAVVKRQLAAVIhlnghcISEIVVAYEPVWAIGTGRTASPEQAQAVHAVLR 191 *********998888888777768999989999***************************** PP TIGR00419 180 dhlkkvskevaesvrvlyGasvtaaedaelaaqldvdGvLlasavlka 227 l+ + e a+ +r+lyG+s++a+++a+l aq+d+dG L+++a+lka lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1454 192 AQLAA-ASEHADRIRLLYGGSMNAGNAAQLLAQPDIDGGLVGGASLKA 238 87775.567799***********************************8 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 7.19 // [ok]
This GapMind analysis is from Sep 17 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