Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_007692221.1 C447_RS06860 triose-phosphate isomerase
Query= BRENDA::Q12UK2 (221 letters) >NCBI__GCF_000336675.1:WP_007692221.1 Length = 215 Score = 217 bits (553), Expect = 1e-61 Identities = 116/214 (54%), Positives = 148/214 (69%), Gaps = 5/214 (2%) Query: 5 IVLNLKTYLEGTGEGAVRIARACKEVGEASGIEIAIAPQFCDIYRVASQVDVPVYSQHLD 64 +++NLK Y V IA +V + SG+ IA+APQ + RVA + V ++QH+ Sbjct: 3 VLVNLKAY----AADPVEIATVAHDVADESGVRIAVAPQTAHLERVA-ETGVETWAQHVS 57 Query: 65 GVGAGSFTGHAFAKCIKDAGAVGTLINHSECRLKLADIEASVTAAKGEGLRTIICTNNIA 124 V GS TG A A+ + DAG VGTLINHSE RLKLAD++ +V AA+ GL T++C NN Sbjct: 58 PVEHGSHTGSALAEAVADAGVVGTLINHSEKRLKLADVDGAVNAAERAGLETVVCANNPD 117 Query: 125 TTAAAAALGPDYVAVEPPELIGSGIPVSKADPEVVTGSVAAVERIDPAVKVLCGAGISKG 184 AAAALGPD VAVEPPELIG + VS+ADP++V +VAA E +D +V VLCGAG+S G Sbjct: 118 QVGAAAALGPDAVAVEPPELIGGDVSVSQADPDIVEDAVAAAEAVDDSVDVLCGAGVSTG 177 Query: 185 EDLKAAIELGSVGVLLASGIVKAKDPKAALEDLV 218 EDL AA +LG+ GVLLASG+ KA DP+AAL LV Sbjct: 178 EDLDAAGDLGAEGVLLASGVAKADDPRAALTSLV 211 Lambda K H 0.316 0.134 0.378 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: 175 Number of extensions: 4 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: 221 Length of database: 215 Length adjustment: 22 Effective length of query: 199 Effective length of database: 193 Effective search space: 38407 Effective search space used: 38407 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: 45 (21.9 bits)
Align candidate WP_007692221.1 C447_RS06860 (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.4138573.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-53 167.6 10.4 2.3e-53 167.4 10.4 1.1 1 NCBI__GCF_000336675.1:WP_007692221.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000336675.1:WP_007692221.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 167.4 10.4 2.3e-53 2.3e-53 16 228 .] 14 201 .. 2 201 .. 0.95 Alignments for each domain: == domain 1 score: 167.4 bits; conditional E-value: 2.3e-53 TIGR00419 16 elevaklaeevaseagvevavappfvdldvvkdeveseiqvaAqnvdavksGaftGeisAemlkdlGakgvli 88 e+a++a++va+e+gv +avap+ +l++v++ ++ Aq+v v+ G++tG+ +Ae+++d+G+ g+li NCBI__GCF_000336675.1:WP_007692221.1 14 PVEIATVAHDVADESGVRIAVAPQTAHLERVAET---GVETWAQHVSPVEHGSHTGSALAEAVADAGVVGTLI 83 5689*************************99875...468********************************* PP TIGR00419 89 gHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaaAlepdvvAvEPveliG 161 +HsE+R lk+ad ++ v+ + gl++vvC nn + aaaAl pd vAvEP+eliG NCBI__GCF_000336675.1:WP_007692221.1 84 NHSEKR--LKLAD--VDGAVNAAERAGLETVVCA-------------NNPDQVGAAAALGPDAVAVEPPELIG 139 ******..*****..*******************.............9999999******************* PP TIGR00419 162 tGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdGvLlasavlkae 228 ++vs+A+++ ve+ v +++ v +sv vl+Ga+v+++ed ++a +l+++GvLlas+v ka+ NCBI__GCF_000336675.1:WP_007692221.1 140 GDVSVSQADPDIVEDAVA-----AAEAVDDSVDVLCGAGVSTGEDLDAAGDLGAEGVLLASGVAKAD 201 ******************.....9*****************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (215 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: 15.91 // [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