Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_014149962.1 MEALZ_RS17400 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000968535.2:WP_014149962.1 Length = 390 Score = 342 bits (876), Expect = 2e-98 Identities = 188/392 (47%), Positives = 258/392 (65%), Gaps = 12/392 (3%) Query: 8 DVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK-GE 66 D+DL KRV++R D NVP+K+G V D RI+A+LPTIK+AL GA VIL+SHLGRP+ G Sbjct: 8 DLDLSNKRVLIREDLNVPIKNGKVASDIRIQASLPTIKHALSAGAAVILMSHLGRPEEGV 67 Query: 67 PSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKN 126 S E S+ PVA+ L LLGK V+ + D + E++ GEV+L EN RF+ GE KN Sbjct: 68 YSEEASMKPVAEHLQGLLGKPVRLEKDWI-DGI-----EIQPGEVVLCENVRFNKGEGKN 121 Query: 127 DPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKVTYNP 185 EL K A+L DI V DAFGTAHRA AS +AQF P + AG L+ KE+ L K +P Sbjct: 122 SEELGKKMAALCDIFVMDAFGTAHRAQASTHSVAQFAPIACAGPLLAKELDALGKALESP 181 Query: 186 EKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDL 245 ++P V ++GG+KVS K+ V+ +L +K DR+++GG + TF+ A G VG S E D ID Sbjct: 182 DRPLVAIVGGSKVSTKLTVLESLSQKVDRLIVGGGIANTFIAAAGFPVGKSLYEADLIDE 241 Query: 246 AKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFK 305 A L+++AK G EI +PVD V A++ V ++ D + + + +DIGPET L+ Sbjct: 242 ANRLMDQAKRNGAEIPVPVDVVCAKEFSESAAATVKKVAD-VQDDDLIMDIGPETAALYA 300 Query: 306 QKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKFGL 365 L A T+VWNGP+GVFE D F GT+ ++ AIA + ++ GGGD+ AA++K+G+ Sbjct: 301 DILKSAGTIVWNGPVGVFEFDQFGGGTEALSKAIA---DSSGFSIAGGGDTLAAIDKYGI 357 Query: 366 EDKFSHVSTGGGASLEFLEGKELPGIASIADK 397 E+K S+ STGGGA LEFLEGKELP +A + + Sbjct: 358 EEKVSYTSTGGGAFLEFLEGKELPAVAVLQQR 389 Lambda K H 0.317 0.137 0.386 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: 636 Number of extensions: 39 Number of successful extensions: 6 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: 654 Length of database: 390 Length adjustment: 34 Effective length of query: 620 Effective length of database: 356 Effective search space: 220720 Effective search space used: 220720 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: 52 (24.6 bits)
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