Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_084544715.1 H566_RS0103365 triose-phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >NCBI__GCF_000482785.1:WP_084544715.1 Length = 247 Score = 201 bits (510), Expect = 2e-56 Identities = 112/244 (45%), Positives = 155/244 (63%), Gaps = 8/244 (3%) Query: 6 VMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIMLGAQN 65 V+GNWK+NGS L++ +R EL + G V + P +Y+ A + + S +++GAQ+ Sbjct: 10 VVGNWKMNGSIAANEALLAAVR-ELPRI-GANVGVCAPYVYLPQAVQALDKSAVVVGAQD 67 Query: 66 VDLNL-SGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTPV 124 + + SGAFTGE S AML ++G + +I+GHSERR YH E+DE++A K GL P+ Sbjct: 68 LSAHAASGAFTGEVSGAMLAEVGVRQVIVGHSERRQYHGETDEIVAAKALAALGAGLVPI 127 Query: 125 LCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATPAQAQ 184 +C+GET E +A + EV RQ+ AV+ G E ++AYEPVWAIGTG++A+P QAQ Sbjct: 128 VCVGETLVERDADQAFEVVNRQLGAVMAALGERINE-VLVAYEPVWAIGTGRTASPEQAQ 186 Query: 185 AVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFAV 244 VH IR + A V + YGGSV ASNA+ +FA D+DG L+GGASL A FA Sbjct: 187 EVHASIRAKLGSAGA----VVPVLYGGSVKASNASSIFAMSDVDGGLIGGASLVAGDFAA 242 Query: 245 IVKA 248 IV A Sbjct: 243 IVAA 246 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: 186 Number of extensions: 7 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: 255 Length of database: 247 Length adjustment: 24 Effective length of query: 231 Effective length of database: 223 Effective search space: 51513 Effective search space used: 51513 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_084544715.1 H566_RS0103365 (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.9467.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-61 192.1 6.9 7.1e-61 191.9 6.9 1.0 1 lcl|NCBI__GCF_000482785.1:WP_084544715.1 H566_RS0103365 triose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000482785.1:WP_084544715.1 H566_RS0103365 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 191.9 6.9 7.1e-61 7.1e-61 2 227 .. 10 237 .. 9 238 .. 0.93 Alignments for each domain: == domain 1 score: 191.9 bits; conditional E-value: 7.1e-61 TIGR00419 2 viinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdav.ksGa 68 v++n+K+n+s+ e ++a ++e + g +v+v p+v+l+ ++++++ s + v+Aq++ a+ sGa lcl|NCBI__GCF_000482785.1:WP_084544715.1 10 VVGNWKMNGSIAANEALLAAVREL--PRIGANVGVCAPYVYLPQAVQALDkSAVVVGAQDLSAHaASGA 76 89*******************983..68899******************999*********986268** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137 ftGe+s +ml+++G++ v++gHsErR ++ e+de++++k + gl ++vCvgetl er+a + +++ lcl|NCBI__GCF_000482785.1:WP_084544715.1 77 FTGEVSGAMLAEVGVRQVIVGHSERRQYHGETDEIVAAKALAALGAGLVPIVCVGETLVERDADQAFEV 145 ********************************************************************* PP TIGR00419 138 vattaaaaA......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGas 200 v+++ +a+ +++++vA+EPv++iGtG+++s+ +a++v++s+r l + v vlyG+s lcl|NCBI__GCF_000482785.1:WP_084544715.1 146 VNRQLGAVMaalgerINEVLVAYEPVWAIGTGRTASPEQAQEVHASIRAKLGSAG----AVVPVLYGGS 210 ****9886557999999*******************************5555444....4578****** PP TIGR00419 201 vtaaedaelaaqldvdGvLlasavlka 227 v+a+++ +a dvdG L+++a+l a lcl|NCBI__GCF_000482785.1:WP_084544715.1 211 VKASNASSIFAMSDVDGGLIGGASLVA 237 ************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (247 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: 6.09 // [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