Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate SMc01023 SMc01023 triosephosphate isomerase
Query= SwissProt::Q8L1Z5 (254 letters) >FitnessBrowser__Smeli:SMc01023 Length = 256 Score = 295 bits (754), Expect = 8e-85 Identities = 147/254 (57%), Positives = 188/254 (74%) Query: 1 MSPNIRPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGG 60 M+P+IRP +AGNWKMNGT SL +++A+A G+ DL +ALIC PATLL A + Sbjct: 1 MTPDIRPLVAGNWKMNGTRASLDQIKAMAEGVKGDLSARVDALICPPATLLYVATALCDD 60 Query: 61 ENILLGGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAA 120 +++G Q+CH G +TG++SA M+ + +HVI+GHSERRT + E DA+VRAK +AA Sbjct: 61 SPLMIGAQDCHQKQSGAHTGEVSAEMVADCFGTHVIVGHSERRTDHGEGDALVRAKTEAA 120 Query: 121 WRAGLVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTA 180 A LVA++CVGET EERK+ + LD+L RQL SLPD ATAEN +IAYEPVWA+GTG T Sbjct: 121 HGADLVAIVCVGETEEERKAGRTLDILKRQLSESLPDQATAENTVIAYEPVWAIGTGLTP 180 Query: 181 TSADVAEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLK 240 T +DV E HAF+ ++ SRFG EG K+R+LYGGSVKPSNA EL+ A+V+GALIGGASLK Sbjct: 181 TVSDVEEAHAFMRRELVSRFGAEGGKMRILYGGSVKPSNAKELMGVANVDGALIGGASLK 240 Query: 241 AIDFLTICDVYRKL 254 A DFL I Y +L Sbjct: 241 ADDFLAIYRAYEEL 254 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: 252 Number of extensions: 12 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: 254 Length of database: 256 Length adjustment: 24 Effective length of query: 230 Effective length of database: 232 Effective search space: 53360 Effective search space used: 53360 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: 47 (22.7 bits)
Align candidate SMc01023 SMc01023 (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.26709.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.4e-54 168.6 0.4 1.1e-53 168.4 0.4 1.0 1 lcl|FitnessBrowser__Smeli:SMc01023 SMc01023 triosephosphate isomera Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc01023 SMc01023 triosephosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 168.4 0.4 1.1e-53 1.1e-53 1 228 [] 8 242 .. 8 242 .. 0.88 Alignments for each domain: == domain 1 score: 168.4 bits; conditional E-value: 1.1e-53 TIGR00419 1 lviinfKlnesvgkvelevaklaeevase..agvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 lv +n+K+n+++ + ++ + +ae v + a v + pp l v++ + s ++++Aq+++ ++sGa+tGe lcl|FitnessBrowser__Smeli:SMc01023 8 LVAGNWKMNGTRASLDQ-IKAMAEGVKGDlsARVDALICPPATLLYVATALCDdSPLMIGAQDCHQKQSGAHTGE 81 799*******9998775.55666666664114566679999988888888877789******************* PP TIGR00419 73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaaA. 146 +sAem++d+ +v++gHsErR+ + e d l+ +k ++ +l ++vCvget+eer+a+rt++ ++++ + lcl|FitnessBrowser__Smeli:SMc01023 82 VSAEMVADCFGTHVIVGHSERRTDHGEGDALVRAKTEAAHGADLVAIVCVGETEEERKAGRTLDILKRQLSESLp 156 ****************************************************************99888653223 PP TIGR00419 147 ....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdG 217 e+ v+A+EPv++iGtG + + + e+ ++++r l ++r+lyG+sv+ ++++el+ +vdG lcl|FitnessBrowser__Smeli:SMc01023 157 dqatAENTVIAYEPVWAIGTGLTPTVSDVEEAHAFMRRELVSRFGAEGGKMRILYGGSVKPSNAKELMGVANVDG 231 33349********************************77666444446689************************ PP TIGR00419 218 vLlasavlkae 228 +L+++a+lka+ lcl|FitnessBrowser__Smeli:SMc01023 232 ALIGGASLKAD 242 *********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (256 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 9.45 // [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