Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_037153750.1 RHSP_RS21965 triose-phosphate isomerase
Query= SwissProt::Q8L1Z5 (254 letters) >NCBI__GCF_000359745.1:WP_037153750.1 Length = 256 Score = 268 bits (684), Expect = 1e-76 Identities = 131/253 (51%), Positives = 174/253 (68%) Query: 1 MSPNIRPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGG 60 M+ +RP +AGNWKMNGT SL +++AIA G+ + L + L+C PATLL A + Sbjct: 1 MTKTVRPLLAGNWKMNGTRASLDQIKAIADGVKAPLSEKIDTLLCPPATLLYVATALCDD 60 Query: 61 ENILLGGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAA 120 + +G Q+CH G +TGDISA M+ + +HVI+GHSERR + ESD +VRAK QAA Sbjct: 61 SPLAIGAQDCHQQVSGAHTGDISAEMIADCFGTHVIVGHSERRRNHAESDMLVRAKAQAA 120 Query: 121 WRAGLVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTA 180 AGL+A+IC+GET ER S + LDVL R+L GS+PDG++A+ ++AYEPVWA+GTG Sbjct: 121 HDAGLIAIICIGETAYERNSGQTLDVLKRELIGSIPDGSSAQTTVVAYEPVWAIGTGVVP 180 Query: 181 TSADVAEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLK 240 T +V E HAFI ++ RFG EGA +R+LYGGSV +NA +LL HVNG L+GG SLK Sbjct: 181 TQENVEEAHAFIRAELIQRFGKEGANMRILYGGSVSGANARDLLEVPHVNGVLVGGQSLK 240 Query: 241 AIDFLTICDVYRK 253 A DFL I + + Sbjct: 241 AADFLAIYAAFER 253 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: 231 Number of extensions: 9 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 WP_037153750.1 RHSP_RS21965 (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.3002219.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-51 161.7 0.4 1.5e-51 161.5 0.4 1.0 1 NCBI__GCF_000359745.1:WP_037153750.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000359745.1:WP_037153750.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 161.5 0.4 1.5e-51 1.5e-51 2 227 .. 9 241 .. 8 242 .. 0.87 Alignments for each domain: == domain 1 score: 161.5 bits; conditional E-value: 1.5e-51 TIGR00419 2 viinfKlnesvgkvelevaklaeevase..agvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftG 71 + +n+K+n+++ + ++ + +a+ v + +++ + pp l v++ + s + ++Aq+++ + sGa+tG NCBI__GCF_000359745.1:WP_037153750.1 9 LAGNWKMNGTRASLDQ-IKAIADGVKAPlsEKIDTLLCPPATLLYVATALCDdSPLAIGAQDCHQQVSGAHTG 80 679******9988765.56666666554113455567888888887777777789****************** PP TIGR00419 72 eisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaa 144 +isAem++d+ +v++gHsErR ++e+d l+ +k +++ gl +++C+get er++++t+++++++ NCBI__GCF_000359745.1:WP_037153750.1 81 DISAEMIADCFGTHVIVGHSERRRNHAESDMLVRAKAQAAHDAGLIAIICIGETAYERNSGQTLDVLKRELIG 153 *****************************************************************99876543 PP TIGR00419 145 aA.....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaq 212 + vvA+EPv++iGtG++ ++ + e+ ++++r l + + ++r+lyG+sv++a++ +l NCBI__GCF_000359745.1:WP_037153750.1 154 SIpdgssAQTTVVAYEPVWAIGTGVVPTQENVEEAHAFIRAELIQRFGKEGANMRILYGGSVSGANARDLLEV 226 33467668999*****************************88877555557789******************* PP TIGR00419 213 ldvdGvLlasavlka 227 + v+GvL+++ +lka NCBI__GCF_000359745.1:WP_037153750.1 227 PHVNGVLVGGQSLKA 241 **************8 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: 13.87 // [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