Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_011384224.1 AMB_RS09205 triose-phosphate isomerase
Query= SwissProt::Q8L1Z5 (254 letters) >NCBI__GCF_000009985.1:WP_011384224.1 Length = 251 Score = 227 bits (578), Expect = 2e-64 Identities = 119/248 (47%), Positives = 159/248 (64%), Gaps = 7/248 (2%) Query: 6 RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLF---EALICVPATLLSRAFDILGGEN 62 R IAGNWKMNG + A+A G++ L + L+C P TL++ D L G Sbjct: 5 RKLIAGNWKMNGLK---ADGLALAKGLADKLASASPNCDMLVCPPFTLIAPVADALAGSK 61 Query: 63 ILLGGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWR 122 + +GGQ+CH G +TGD S ML + G + I+GHSERRT + E+D +V+AK AA Sbjct: 62 LAVGGQDCHAKTSGAHTGDTSPAMLADLGCKYAIVGHSERRTDHAETDNVVKAKAAAALS 121 Query: 123 AGLVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATS 182 AGLVA++C+GETL +R + + ++V QL GSLP+GA A N +IAYEPVWA+GTG AT Sbjct: 122 AGLVAIVCIGETLAQRDAGQTIEVNRSQLNGSLPEGANAANTVIAYEPVWAIGTGRVATP 181 Query: 183 ADVAEVHAFIHHKMHSRFG-DEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKA 241 A EVHA I ++ G +E K+R+LYGGS+KP NA ELL+ V+G LIGGA+LK Sbjct: 182 AQAQEVHAAIRAELARLVGAEEAGKMRILYGGSMKPDNAKELLALPDVDGGLIGGAALKV 241 Query: 242 IDFLTICD 249 DF I + Sbjct: 242 ADFWAIAE 249 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: 224 Number of extensions: 11 Number of successful extensions: 3 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: 251 Length adjustment: 24 Effective length of query: 230 Effective length of database: 227 Effective search space: 52210 Effective search space used: 52210 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 WP_011384224.1 AMB_RS09205 (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.15232.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-64 204.5 0.8 1.3e-64 204.2 0.8 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011384224.1 AMB_RS09205 triose-phosphate iso Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011384224.1 AMB_RS09205 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 204.2 0.8 1.3e-64 1.3e-64 1 226 [. 7 240 .. 7 242 .. 0.94 Alignments for each domain: == domain 1 score: 204.2 bits; conditional E-value: 1.3e-64 TIGR00419 1 lviinfKlnesvgkvelevaklaeevasea.gvevavappfvdldvvkdeve.seiqvaAqnvdavksG 67 l+ +n+K+n+ + + la+++as + ++ + v ppf + v+d++ s++ v+ q+++a++sG lcl|NCBI__GCF_000009985.1:WP_011384224.1 7 LIAGNWKMNGLKADGLALAKGLADKLASASpNCDMLVCPPFTLIAPVADALAgSKLAVGGQDCHAKTSG 75 689*******99988888888******98648*******************99**************** PP TIGR00419 68 aftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartin 136 a+tG++s +ml+dlG+k+ ++gHsErR+ ++e+d+++++k a + gl ++vC+getl++r+a++ti+ lcl|NCBI__GCF_000009985.1:WP_011384224.1 76 AHTGDTSPAMLADLGCKYAIVGHSERRTDHAETDNVVKAKAAAALSAGLVAIVCIGETLAQRDAGQTIE 144 ********************************************************************9 PP TIGR00419 137 nvattaaaaA.....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGa 199 + + + + v+A+EPv++iGtG+++++A+a++v++ +r l++ v +e a ++r+lyG+ lcl|NCBI__GCF_000009985.1:WP_011384224.1 145 VNRSQLNGSLpeganAANTVIAYEPVWAIGTGRVATPAQAQEVHAAIRAELARlVGAEEAGKMRILYGG 213 7766644322344448899**********************************99************** PP TIGR00419 200 svtaaedaelaaqldvdGvLlasavlk 226 s++ +++el a +dvdG L+++a lk lcl|NCBI__GCF_000009985.1:WP_011384224.1 214 SMKPDNAKELLALPDVDGGLIGGAALK 240 *************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (251 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: 10.52 // [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