Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_076477790.1 BW971_RS06715 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_900156495.1:WP_076477790.1 Length = 405 Score = 355 bits (910), Expect = e-102 Identities = 197/390 (50%), Positives = 259/390 (66%), Gaps = 13/390 (3%) Query: 11 LKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPSP 69 + G+ V++R D NVP+ D G + D RI A++PT+ L+ GAKV++ +HLGRPKG P Sbjct: 15 VSGRGVLVRSDLNVPLDDHGQITDPGRILASVPTLTALLDAGAKVVVTAHLGRPKGAPEA 74 Query: 70 EFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET-KNDP 128 ++SLAPVA+RLS LG+ V+ VVG + E L +G++LL+EN RF P ET K++ Sbjct: 75 KYSLAPVAERLSAELGRNVQLAGDVVGQDALARSEGLTDGDILLVENVRFDPRETSKDEA 134 Query: 129 ELAKFWASLADI------HVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVT 182 E +L ++ V+D FG HR AS +A+ +P AG L+ E++ L+K+T Sbjct: 135 ERTALAEALVELVGEDGAFVSDGFGVVHRKQASVYDVAKLLPHYAGELVAAEVEVLTKLT 194 Query: 183 YNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDK 242 E+P+ VVLGG+KVSDKIGVI L K D ++IGG M FTFL A G VG S +++D+ Sbjct: 195 DEVERPFAVVLGGSKVSDKIGVIEALAPKVDTLVIGGGMAFTFLAAEGLNVGDSLLQQDQ 254 Query: 243 IDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIE 302 I++ K LLE+ G I LPVD V+A E KVV + IP+GWMGLDIGPE+++ Sbjct: 255 IEVCKGLLERF---GDVIHLPVDVVVASAFAADAESKVVPAQE-IPDGWMGLDIGPESVK 310 Query: 303 LFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNK 362 F LS AKT+ WNGP GVFE FA+GT+ VA AI T GA TVVGGGDSAAAV Sbjct: 311 RFAAVLSGAKTIFWNGPSGVFEFAKFADGTRGVAEAIIETTRHGAFTVVGGGDSAAAVRT 370 Query: 363 FGL-EDKFSHVSTGGGASLEFLEGKELPGI 391 GL ED FSH+STGGGASLE+LEGK+LPG+ Sbjct: 371 LGLPEDGFSHISTGGGASLEYLEGKDLPGL 400 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: 641 Number of extensions: 36 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: 405 Length adjustment: 35 Effective length of query: 619 Effective length of database: 370 Effective search space: 229030 Effective search space used: 229030 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 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