Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate Ga0059261_0254 Ga0059261_0254 triosephosphate isomerase (EC 5.3.1.1)
Query= SwissProt::Q8L1Z5 (254 letters) >FitnessBrowser__Korea:Ga0059261_0254 Length = 248 Score = 221 bits (564), Expect = 8e-63 Identities = 123/245 (50%), Positives = 163/245 (66%), Gaps = 5/245 (2%) Query: 6 RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENILL 65 R +AGNWKM+G +L E+ AIA + G +A +CVPATL++ A + + + Sbjct: 3 RKLVAGNWKMHGLIAALPEIEAIAQAAAVTPG--VDAALCVPATLIAPAVTVAA--RMPI 58 Query: 66 GGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAGL 125 GGQ+CH D G +TG ISA ML+EAGA+ I+GHSERR E+DA V+ K +AA R GL Sbjct: 59 GGQDCHAADQGAHTGCISAAMLREAGAALTIVGHSERRANQGETDADVKGKAEAAHRHGL 118 Query: 126 VALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSADV 185 A++CVGETLE+R + + V+T QL GS+P+GA A+ + IAYEPVWA+GTG T T ADV Sbjct: 119 NAILCVGETLEQRDAGQAEAVVTAQLAGSMPEGAAADWLSIAYEPVWAIGTGRTPTEADV 178 Query: 186 AEVHAFIHHKMHSRFGDE-GAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAIDF 244 A +H I K+ G E A +R+LYGGSV +NA LL A V+GAL+GGASL A F Sbjct: 179 AAMHGAIRAKLTELLGGETAAAMRVLYGGSVNGANAASLLGCADVDGALVGGASLTAEKF 238 Query: 245 LTICD 249 + I + Sbjct: 239 VPIIE 243 Lambda K H 0.320 0.137 0.403 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: 233 Number of extensions: 8 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: 254 Length of database: 248 Length adjustment: 24 Effective length of query: 230 Effective length of database: 224 Effective search space: 51520 Effective search space used: 51520 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 bits)
Align candidate Ga0059261_0254 Ga0059261_0254 (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.5113.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-50 158.4 5.8 1.5e-50 158.2 5.8 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_0254 Ga0059261_0254 triosephosphate i Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_0254 Ga0059261_0254 triosephosphate isomerase (EC 5.3.1.1) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 158.2 5.8 1.5e-50 1.5e-50 1 228 [] 5 236 .. 5 236 .. 0.89 Alignments for each domain: == domain 1 score: 158.2 bits; conditional E-value: 1.5e-50 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeveseiqvaAqnvdavksGaf 69 lv +n+K+++ + e+ +a+ a + gv a+ +p + ++ + +++++ q+++a ++Ga+ lcl|FitnessBrowser__Korea:Ga0059261_0254 5 LVAGNWKMHGLIAAL-PEIEAIAQAAAVTPGVDAALCVPATLIAPAVTVAA-RMPIGGQDCHAADQGAH 71 799******999876.57899***99********99988877765554333.6**************** PP TIGR00419 70 tGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnv 138 tG isA+ml+++Ga+ +++gHsErR+ e+d ++ k ++ gl++++Cvgetle+r+a++ +v lcl|FitnessBrowser__Korea:Ga0059261_0254 72 TGCISAAMLREAGAALTIVGHSERRANQGETDADVKGKAEAAHRHGLNAILCVGETLEQRDAGQAEAVV 140 *******************************999***************************99775555 PP TIGR00419 139 attaaa.....aAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasv 201 + + a aA + +A+EPv++iGtG++ ++A+ ++++ +r l++ e a +rvlyG+sv lcl|FitnessBrowser__Korea:Ga0059261_0254 141 TAQLAGsmpegAAADWLSIAYEPVWAIGTGRTPTEADVAAMHGAIRAKLTElLGGETAAAMRVLYGGSV 209 544432222224566778*******************************998999************** PP TIGR00419 202 taaedaelaaqldvdGvLlasavlkae 228 ++a++a l dvdG+L+++a+l ae lcl|FitnessBrowser__Korea:Ga0059261_0254 210 NGANAASLLGCADVDGALVGGASLTAE 236 ************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (248 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: 10.13 // [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