Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_012469676.1 GLOV_RS08025 triose-phosphate isomerase
Query= SwissProt::Q8XKU1 (248 letters) >NCBI__GCF_000020385.1:WP_012469676.1 Length = 251 Score = 257 bits (656), Expect = 2e-73 Identities = 130/249 (52%), Positives = 172/249 (69%), Gaps = 1/249 (0%) Query: 1 MRTPIIAGNWKMHYTIDEAVKLVEELKPLVKDAK-CEVVVCPTFVCLDAVKKAVEGTNIK 59 MRTP+IAGNWK+ T+ +A L++EL PLV D K E+VV P F ++ V KA T +K Sbjct: 1 MRTPLIAGNWKLFKTLADATALIDELVPLVSDVKDVEIVVAPVFTAINTVAKAAGKTGVK 60 Query: 60 VGAQNMHFEEKGAFTGEIAPRMLEAMNIDYVIIGHSERREYFNETDETCNKKVKAAFAHN 119 V AQ+ ++E++GAFTGE++P++L+ +VIIGHSERR+YF ETD T N K KAA Sbjct: 61 VAAQDCYWEDEGAFTGEVSPKLLKDAGCSHVIIGHSERRQYFGETDGTVNLKTKAAIRAG 120 Query: 120 LTPILCCGETLEQRENGTTNDVIKAQITADLEGLTKEQAEKVVIAYEPIWAIGTGKTATS 179 LT +LC GE+L QRE+ T VI+ Q+ L + + ++V+AYEP+WAIGTGKTA+ Sbjct: 121 LTVLLCVGESLAQRESNDTFKVIETQVRGGLADIPAAELTQIVVAYEPVWAIGTGKTASD 180 Query: 180 DQANETIAAIRAMVAEMFGQEVADKVRIQYGGSVKPNTIAEQMAKSDIDGALVGGASLVA 239 QA E A IR +VA+++G AD +RI YGGSVKP I M++ DIDGALVGGASL A Sbjct: 181 AQAQEVHAFIRTLVAQIYGPSEADAMRILYGGSVKPENIKGLMSQPDIDGALVGGASLKA 240 Query: 240 ADFAQIVNY 248 FA IV + Sbjct: 241 ESFAGIVRF 249 Lambda K H 0.316 0.131 0.376 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: 169 Number of extensions: 6 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: 248 Length of database: 251 Length adjustment: 24 Effective length of query: 224 Effective length of database: 227 Effective search space: 50848 Effective search space used: 50848 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 46 (22.3 bits)
Align candidate WP_012469676.1 GLOV_RS08025 (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.3268.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-66 207.9 0.9 1.1e-65 207.7 0.9 1.0 1 lcl|NCBI__GCF_000020385.1:WP_012469676.1 GLOV_RS08025 triose-phosphate is Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020385.1:WP_012469676.1 GLOV_RS08025 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 207.7 0.9 1.1e-65 1.1e-65 1 228 [] 5 241 .. 5 241 .. 0.95 Alignments for each domain: == domain 1 score: 207.7 bits; conditional E-value: 1.1e-65 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 l+ +n+Kl ++ + ++ +l v+++++ve++vap f +++v++++ + ++vaAq++ + Ga lcl|NCBI__GCF_000020385.1:WP_012469676.1 5 LIAGNWKLFKTLADATALIDELVPLVSDVKDVEIVVAPVFTAINTVAKAAGkTGVKVAAQDCYWEDEGA 73 689********************************************9998799*************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137 ftGe+s ++lkd+G+ +v+igHsErR ++ e+d ++ k + gl++++Cvge+l++re+ t+++ lcl|NCBI__GCF_000020385.1:WP_012469676.1 74 FTGEVSPKLLKDAGCSHVIIGHSERRQYFGETDGTVNLKTKAAIRAGLTVLLCVGESLAQRESNDTFKV 142 ********************************************************************* PP TIGR00419 138 vattaa.aaA......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyG 198 + t+ A l++ vvA+EPv++iGtGk++s A+a++v++++r +++ + a+ +r+lyG lcl|NCBI__GCF_000020385.1:WP_012469676.1 143 IETQVRgGLAdipaaeLTQIVVAYEPVWAIGTGKTASDAQAQEVHAFIRTLVAQiYGPSEADAMRILYG 211 *998642344566667*********************************999996678999******** PP TIGR00419 199 asvtaaedaelaaqldvdGvLlasavlkae 228 +sv+ ++ + l+ q+d+dG+L+++a+lkae lcl|NCBI__GCF_000020385.1:WP_012469676.1 212 GSVKPENIKGLMSQPDIDGALVGGASLKAE 241 ****************************97 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.95 // [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