Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_106710611.1 CU102_RS08140 triose-phosphate isomerase
Query= SwissProt::Q8L1Z5 (254 letters) >NCBI__GCF_003010955.1:WP_106710611.1 Length = 255 Score = 318 bits (816), Expect = 5e-92 Identities = 156/254 (61%), Positives = 193/254 (75%) Query: 1 MSPNIRPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGG 60 M+P++RP +AGNWKMNGTGESL ELR I +S +G +ALICVPATL+ RA + G Sbjct: 1 MTPDVRPLVAGNWKMNGTGESLDELRMIVNRPNSAIGEKIDALICVPATLVFRAAQSVEG 60 Query: 61 ENILLGGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAA 120 E + +GGQ+CHF G +TGDISA MLK+AGASHVI+GHSERRT + E+DA+V AK +A Sbjct: 61 EALSIGGQDCHFKKSGAHTGDISAEMLKDAGASHVIVGHSERRTDHGETDAVVNAKAKAG 120 Query: 121 WRAGLVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTA 180 W AGLVA+ICVGET +RK+ LDV++ QL GS+PD A A N IIAYEPVWA+GTG T Sbjct: 121 WDAGLVAIICVGETEAQRKAGSTLDVISTQLAGSIPDNANARNTIIAYEPVWAIGTGLTP 180 Query: 181 TSADVAEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLK 240 T+ DV +VHA I + RF +G K+R+LYGGSVKP+NA ELL A+V+GAL+GGASLK Sbjct: 181 TADDVQQVHASIRAALEKRFAADGGKMRILYGGSVKPANAVELLGVANVDGALVGGASLK 240 Query: 241 AIDFLTICDVYRKL 254 A DFL IC+ Y L Sbjct: 241 AADFLAICEAYHSL 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: 280 Number of extensions: 8 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: 255 Length adjustment: 24 Effective length of query: 230 Effective length of database: 231 Effective search space: 53130 Effective search space used: 53130 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_106710611.1 CU102_RS08140 (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.2991469.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-56 178.3 3.1 1.2e-56 178.1 3.1 1.0 1 NCBI__GCF_003010955.1:WP_106710611.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010955.1:WP_106710611.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 178.1 3.1 1.2e-56 1.2e-56 1 227 [. 8 241 .. 8 242 .. 0.89 Alignments for each domain: == domain 1 score: 178.1 bits; conditional E-value: 1.2e-56 TIGR00419 1 lviinfKlne...svgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaf 69 lv +n+K+n+ s+ + ++v++ + + ++ + + v v+ ++++ ve ++++ q+++ +ksGa+ NCBI__GCF_003010955.1:WP_106710611.1 8 LVAGNWKMNGtgeSLDELRMIVNRPNSAIGEKIDALICVPATLVF--RAAQSVEgEALSIGGQDCHFKKSGAH 78 799****99711245666778888888888888877777665555..66677775689*************** PP TIGR00419 70 tGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvatta 142 tG+isAemlkd+Ga +v++gHsErR+ + e+d ++++k + gl +++Cvget+++r+a++t++++ t+ NCBI__GCF_003010955.1:WP_106710611.1 79 TGDISAEMLKDAGASHVIVGHSERRTDHGETDAVVNAKAKAGWDAGLVAIICVGETEAQRKAGSTLDVISTQL 151 **********************************************************************998 PP TIGR00419 143 aaaA.....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaela 210 a + ++A+EPv++iGtG + + + ++v++s+r l+k + ++r+lyG+sv+ a+++el NCBI__GCF_003010955.1:WP_106710611.1 152 AGSIpdnanARNTIIAYEPVWAIGTGLTPTADDVQQVHASIRAALEKRFAADGGKMRILYGGSVKPANAVELL 224 765456666999******************************9999977777889****************** PP TIGR00419 211 aqldvdGvLlasavlka 227 +vdG+L+++a+lka NCBI__GCF_003010955.1:WP_106710611.1 225 GVANVDGALVGGASLKA 241 ****************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (255 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: 12.57 // [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