Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate H281DRAFT_04564 H281DRAFT_04564 triosephosphate isomerase
Query= BRENDA::P0A858 (255 letters) >FitnessBrowser__Burk376:H281DRAFT_04564 Length = 259 Score = 221 bits (562), Expect = 2e-62 Identities = 123/255 (48%), Positives = 155/255 (60%), Gaps = 2/255 (0%) Query: 2 RHPLVMGNWKLNGSRHMVHELVSNLRKELAGV-AGCAVAIAPPEMYIDMAKREAEGSHIM 60 R LV+GNWK++G L+ + K A + A V + P Y+ A+ EGS ++ Sbjct: 5 RAKLVVGNWKMHGCLADNAGLLQAVAKGAAELPADVRVGVCVPSPYLAQAQSLLEGSRVV 64 Query: 61 LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120 G Q++ GA+TGE +A M+ D A + I+GHSERR YH+ES EL+A K E G Sbjct: 65 WGVQDISAFTHGAYTGEVAAQMVADFSAAFAIVGHSERRAYHRESAELVAVKTQRALEAG 124 Query: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP 180 LTP++C+GET E EAG TE+V Q+D VL A V+AYEPVWAIGTGKSAT Sbjct: 125 LTPIVCVGETLEEREAGSTEQVVGAQLDEVLAKLSAEEAAHIVVAYEPVWAIGTGKSATS 184 Query: 181 AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD 240 QAQAVH F+R +A A +A V + YGGSV NA ELF+Q DIDG L+GGASLK Sbjct: 185 EQAQAVHAFLRSRLAAKGAGVA-NVTLLYGGSVKPDNAEELFSQQDIDGGLIGGASLKDK 243 Query: 241 AFAVIVKAAEAAKQA 255 F I KAA A A Sbjct: 244 DFLAICKAAAATTAA 258 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: 203 Number of extensions: 10 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: 259 Length adjustment: 24 Effective length of query: 231 Effective length of database: 235 Effective search space: 54285 Effective search space used: 54285 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 H281DRAFT_04564 H281DRAFT_04564 (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.21913.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-62 197.5 2.9 1.7e-62 197.2 2.9 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_04564 H281DRAFT_04564 triosephosphate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_04564 H281DRAFT_04564 triosephosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 197.2 2.9 1.7e-62 1.7e-62 1 227 [. 8 242 .. 8 243 .. 0.94 Alignments for each domain: == domain 1 score: 197.2 bits; conditional E-value: 1.7e-62 TIGR00419 1 lviinfKlnesvgkvelevaklaeevas.eagvevavappfvdldvvkdeve.seiqvaAqnvdav 64 lv++n+K+++ + + + +++ +a+ a+ +a+v v+v +p +l ++ +e s++ + q++ a lcl|FitnessBrowser__Burk376:H281DRAFT_04564 8 LVVGNWKMHGCLADNAGLLQAVAKGAAElPADVRVGVCVPSPYLAQAQSLLEgSRVVWGVQDISAF 73 79**********************8887579*********************999*********** PP TIGR00419 65 ksGaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere 130 + Ga+tGe+ A+m++d+ a++ ++gHsErR++++e+ el++ k r+ e gl+++vCvgetleere lcl|FitnessBrowser__Burk376:H281DRAFT_04564 74 THGAYTGEVAAQMVADFSAAFAIVGHSERRAYHRESAELVAVKTQRALEAGLTPIVCVGETLEERE 139 ****************************************************************** PP TIGR00419 131 .......aartinnvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskev 189 ++ +++ v+ + +a vvA+EPv++iGtGk+++ +a++v++++r l+ + v lcl|FitnessBrowser__Burk376:H281DRAFT_04564 140 agsteqvVGAQLDEVLAKLSAEEAAHIVVAYEPVWAIGTGKSATSEQAQAVHAFLRSRLAAKGAGV 205 666666666667777777777779999*****************************9999999999 PP TIGR00419 190 aesvrvlyGasvtaaedaelaaqldvdGvLlasavlka 227 a +v +lyG+sv+ ++ el+ q d+dG L+++a+lk lcl|FitnessBrowser__Burk376:H281DRAFT_04564 206 A-NVTLLYGGSVKPDNAEELFSQQDIDGGLIGGASLKD 242 8.599*******************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (259 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: 6.85 // [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