Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_048058461.1 MMARC5_RS04490 triose-phosphate isomerase
Query= BRENDA::Q58923 (219 letters) >NCBI__GCF_000016125.1:WP_048058461.1 Length = 221 Score = 324 bits (830), Expect = 9e-94 Identities = 162/214 (75%), Positives = 187/214 (87%) Query: 3 IVINYKTYNESIGNRGLEIAKIAEKVSEESGITIGVAPQFVDLRMIVENVNIPVYAQHID 62 ++INYKTY ESIG GL IAK AEKVS+ESGITIGVAPQF+DLRMI++ VNIPVYAQH+D Sbjct: 5 LIINYKTYTESIGKSGLAIAKAAEKVSDESGITIGVAPQFLDLRMILDEVNIPVYAQHMD 64 Query: 63 NINPGSHTGHILAEAIKDCGCKGTLINHSEKRMLLADIEAVINKCKNLGLETIVCTNNIN 122 +NPGS TGHIL +A+KD G GTL+NHSE+RMLLAD+E I LGL+T+VCTNNI Sbjct: 65 AVNPGSSTGHILPDALKDAGVTGTLLNHSERRMLLADLEKCIEISNKLGLKTVVCTNNIP 124 Query: 123 TSKAVAALSPDYIAVEPPELIGTGIPVSKANPEVVEGTVRAVKEINKDVKVLCGAGISKG 182 SKAV+AL+P IAVEPPELIG+GIPVSKANPEVV GTVR V+EINK+V++LCGAGISKG Sbjct: 125 VSKAVSALNPTSIAVEPPELIGSGIPVSKANPEVVSGTVREVREINKNVEILCGAGISKG 184 Query: 183 EDVKAALDLGAEGVLLASGVVKAKNVEEAIRELI 216 EDVK+AL+LG GVLLASGVVKAKNVE+AIRELI Sbjct: 185 EDVKSALELGTNGVLLASGVVKAKNVEDAIRELI 218 Lambda K H 0.315 0.135 0.374 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: 249 Number of extensions: 4 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: 219 Length of database: 221 Length adjustment: 22 Effective length of query: 197 Effective length of database: 199 Effective search space: 39203 Effective search space used: 39203 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: 42 (22.0 bits) S2: 45 (21.9 bits)
Align candidate WP_048058461.1 MMARC5_RS04490 (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.13291.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-74 236.6 1.4 1.9e-74 236.4 1.4 1.0 1 lcl|NCBI__GCF_000016125.1:WP_048058461.1 MMARC5_RS04490 triose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016125.1:WP_048058461.1 MMARC5_RS04490 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 236.4 1.4 1.9e-74 1.9e-74 3 228 .] 6 208 .. 4 208 .. 0.99 Alignments for each domain: == domain 1 score: 236.4 bits; conditional E-value: 1.9e-74 TIGR00419 3 iinfK.lnesvgkvelevaklaeevaseagvevavappfvdldvvkdeveseiqvaAqnvdavksGaft 70 iin+K + es+gk l +ak ae+v++e+g++++vap+f+dl+++ dev+ i+v+Aq++dav++G+ t lcl|NCBI__GCF_000016125.1:WP_048058461.1 6 IINYKtYTESIGKSGLAIAKAAEKVSDESGITIGVAPQFLDLRMILDEVN--IPVYAQHMDAVNPGSST 72 89************************************************..***************** PP TIGR00419 71 GeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnva 139 G+i+ ++lkd+G+ g+l++HsErR + +ad +ek + +lglk+vvC+ nn+ lcl|NCBI__GCF_000016125.1:WP_048058461.1 73 GHILPDALKDAGVTGTLLNHSERR--MLLAD--LEKCIEISNKLGLKTVVCT-------------NNIP 124 ************************..*****..*******************.............**** PP TIGR00419 140 ttaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedae 208 ++a+ Al+p +AvEP+eliG+G+pvskA++evv ++vr ++e++++v++l+Ga+++++ed++ lcl|NCBI__GCF_000016125.1:WP_048058461.1 125 VSKAVSALNPTSIAVEPPELIGSGIPVSKANPEVVSGTVR-----EVREINKNVEILCGAGISKGEDVK 188 ****************************************.....89********************** PP TIGR00419 209 laaqldvdGvLlasavlkae 228 a++l+ +GvLlas+v+ka+ lcl|NCBI__GCF_000016125.1:WP_048058461.1 189 SALELGTNGVLLASGVVKAK 208 ******************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (221 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: 5.81 // [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