Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_068461599.1 APY04_RS08340 triose-phosphate isomerase
Query= SwissProt::Q8L1Z5 (254 letters) >NCBI__GCF_001541235.1:WP_068461599.1 Length = 253 Score = 257 bits (656), Expect = 2e-73 Identities = 132/250 (52%), Positives = 170/250 (68%), Gaps = 1/250 (0%) Query: 3 PNIRPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGEN 62 P +R +AGNWKMNG + E A+ ++ + +IC PATLL LG Sbjct: 4 PKVRALVAGNWKMNGLRAGIAEAEAVGRALNETPAGA-DVMICPPATLLGPMVAALGDST 62 Query: 63 ILLGGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWR 122 + +GGQ+CH + G +TGD+SA ML +AGA+ VI+GHSERR+++ E D VRAK +AA R Sbjct: 63 VHVGGQDCHVNVSGAFTGDVSAEMLADAGATAVIVGHSERRSLHGELDRDVRAKAEAAHR 122 Query: 123 AGLVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATS 182 AGL A++CVGET ER + V++RQL GSLPDGA A N ++AYEPVWA+GTG T T Sbjct: 123 AGLSAIVCVGETAGERAAALTQTVVSRQLAGSLPDGARAANTVVAYEPVWAIGTGLTPTV 182 Query: 183 ADVAEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAI 242 DVA+VHA I + +RFG EG +R+LYGGSVKP NA EL++ VNGAL+GGASLKA Sbjct: 183 EDVAKVHAAIRKALVARFGAEGQGMRILYGGSVKPQNARELMAVPDVNGALVGGASLKAA 242 Query: 243 DFLTICDVYR 252 DFL I Y+ Sbjct: 243 DFLGIIAAYQ 252 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: 262 Number of extensions: 15 Number of successful extensions: 2 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: 253 Length adjustment: 24 Effective length of query: 230 Effective length of database: 229 Effective search space: 52670 Effective search space used: 52670 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 WP_068461599.1 APY04_RS08340 (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.aa/TIGR00419.hmm # target sequence database: /tmp/gapView.31225.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-52 164.1 3.4 2.7e-52 163.9 3.4 1.0 1 lcl|NCBI__GCF_001541235.1:WP_068461599.1 APY04_RS08340 triose-phosphate i Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001541235.1:WP_068461599.1 APY04_RS08340 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 163.9 3.4 2.7e-52 2.7e-52 1 227 [. 9 241 .. 9 242 .. 0.89 Alignments for each domain: == domain 1 score: 163.9 bits; conditional E-value: 2.7e-52 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdl.dvvkdeveseiqvaAqnvdavksGa 68 lv +n+K+n+ + ++ a ++ +ag v + pp l ++v+ +s ++v+ q+++++ sGa lcl|NCBI__GCF_001541235.1:WP_068461599.1 9 LVAGNWKMNGLRAGIAEAEAVGRALNETPAGADVMICPPATLLgPMVAALGDSTVHVGGQDCHVNVSGA 77 799******999888776555555455689999*****99999345555556***************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137 ftG++sAeml+d+Ga v++gHsErRsl+ e d + +k ++ gl ++vCvget er aa t + lcl|NCBI__GCF_001541235.1:WP_068461599.1 78 FTGDVSAEMLADAGATAVIVGHSERRSLHGELDRDVRAKAEAAHRAGLSAIVCVGETAGERAAALTQTV 146 ****************************************************************99999 PP TIGR00419 138 vattaaaaA.....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasv 201 v ++ a + vvA+EPv++iGtG + + + v++ +r l + +r+lyG+sv lcl|NCBI__GCF_001541235.1:WP_068461599.1 147 VSRQLAGSLpdgarAANTVVAYEPVWAIGTGLTPTVEDVAKVHAAIRKALVARFGAEGQGMRILYGGSV 215 99887755456666899******************************77666555557789******** PP TIGR00419 202 taaedaelaaqldvdGvLlasavlka 227 + +++ el+a +dv+G+L+++a+lka lcl|NCBI__GCF_001541235.1:WP_068461599.1 216 KPQNARELMAVPDVNGALVGGASLKA 241 *************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (253 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: 9.91 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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