Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_013076102.1 BTUS_RS10775 triose-phosphate isomerase
Query= SwissProt::Q4MQ55 (251 letters) >NCBI__GCF_000092905.1:WP_013076102.1 Length = 268 Score = 234 bits (597), Expect = 1e-66 Identities = 118/250 (47%), Positives = 168/250 (67%), Gaps = 3/250 (1%) Query: 2 RKPIIAGNWKMNKTLSEAVSFVEEVKGQIPAASA-VDAVVCSPALFLERLVAAT-EGTDL 59 RKP++A NWKMNKT EA++F E G++ S V+ V+C P L L A + Sbjct: 5 RKPLLAANWKMNKTPEEALAFWREFSGRLSGESERVEVVICPPYTALPALDGANLRARGV 64 Query: 60 QVGAQNMHFEKNGAFTGEISPVALSDLKVGYVVLGHSERREMFAETDESVNKKTIAAFEH 119 +GAQN+H+E GAFTGE+SP L + +V++GHSERR F E+DE+V +K AA + Sbjct: 65 YLGAQNVHWEPRGAFTGEVSPGMLRAVGCSHVIVGHSERRAYFGESDEAVQRKLQAALDE 124 Query: 120 GLTPIVCCGETLEERESGKTFDLVAGQVTKALAGLTEEQVKATVIAYEPIWAIGTGKSSS 179 G+TPI+C GETLE+R +G+ ++VA Q+T AL GL + V+AYEP+WAIGTG+S+ Sbjct: 125 GMTPILCVGETLEQRTAGRAEEVVAAQLTAALEGLDTGRAARVVVAYEPVWAIGTGRSAE 184 Query: 180 SADANEVCAHIRKVVAEAVSPEAAEAVRIQYGGSVKPENIKEYMAQSDIDGALVGGASLE 239 + DA E+ A +R+ + + P AAE +RI YGGSV P+N +++A++++DG LVG ASL Sbjct: 185 ARDAGEMAAAVRRRLRDLAGP-AAEEIRILYGGSVAPDNFVQFLAEAEVDGGLVGTASLR 243 Query: 240 PASFLGLLGA 249 P SF L+ A Sbjct: 244 PESFFALVAA 253 Lambda K H 0.313 0.129 0.360 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: 188 Number of extensions: 7 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: 251 Length of database: 268 Length adjustment: 24 Effective length of query: 227 Effective length of database: 244 Effective search space: 55388 Effective search space used: 55388 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 47 (22.7 bits)
Align candidate WP_013076102.1 BTUS_RS10775 (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.11281.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-56 177.8 0.0 1.7e-56 177.6 0.0 1.0 1 lcl|NCBI__GCF_000092905.1:WP_013076102.1 BTUS_RS10775 triose-phosphate is Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092905.1:WP_013076102.1 BTUS_RS10775 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 177.6 0.0 1.7e-56 1.7e-56 2 228 .] 9 245 .. 8 245 .. 0.94 Alignments for each domain: == domain 1 score: 177.6 bits; conditional E-value: 1.7e-56 TIGR00419 2 viinfKlnesvgkvelevaklaeevasea.gvevavappfvdldvvk.deve.seiqvaAqnvdavksG 67 + n+K+n + ++ + + +++e+ vev++ pp+ l+ + +++ + ++Aqnv+ G lcl|NCBI__GCF_000092905.1:WP_013076102.1 9 LAANWKMNKTPEEALAFWREFSGRLSGESeRVEVVICPPYTALPALDgANLRaRGVYLGAQNVHWEPRG 77 578**********************9876269************98724566568************** PP TIGR00419 68 aftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartin 136 aftGe+s ml+ +G+ +v++gHsErR+++ e+de ++ k+ + + g+++++Cvgetle+r a+r + lcl|NCBI__GCF_000092905.1:WP_013076102.1 78 AFTGEVSPGMLRAVGCSHVIVGHSERRAYFGESDEAVQRKLQAALDEGMTPILCVGETLEQRTAGRAEE 146 ********************************************************************9 PP TIGR00419 137 nvattaaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyG 198 +va + +aa +vvA+EPv++iGtG+++ +a ++ + vr l+ + ae++r+lyG lcl|NCBI__GCF_000092905.1:WP_013076102.1 147 VVAAQLTAALegldtgrAARVVVAYEPVWAIGTGRSAEARDAGEMAAAVRRRLRDLAGPAAEEIRILYG 215 999998888789888888899************************************************ PP TIGR00419 199 asvtaaedaelaaqldvdGvLlasavlkae 228 +sv+ + ++ a+ +vdG L+++a+l++e lcl|NCBI__GCF_000092905.1:WP_013076102.1 216 GSVAPDNFVQFLAEAEVDGGLVGTASLRPE 245 ***************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (268 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: 8.80 // [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