Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_005455727.1 SACCYDRAFT_RS09585 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000244975.1:WP_005455727.1 Length = 402 Score = 372 bits (956), Expect = e-107 Identities = 206/396 (52%), Positives = 266/396 (67%), Gaps = 15/396 (3%) Query: 11 LKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPSPE 70 +KG+RV++R D NVP+ + DD R+RAALP+++ E GA+VI+ +HLGRPKG P P Sbjct: 14 VKGRRVLVRADLNVPLDGQKITDDGRVRAALPSVRALSEAGARVIVTAHLGRPKGAPDPA 73 Query: 71 FSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDP-- 128 FSL PVA RL ELLG EV VVG++ K AV L +G V+LLEN RF ET Sbjct: 74 FSLRPVADRLGELLGTEVSLAGDVVGEQAKAAVAALGDGGVVLLENVRFDARETSKSEAE 133 Query: 129 --ELAKFWASLA---DIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTY 183 ELA+ A+L V+D FG HR AS +A+ +P+ AG L+ E++ L +T Sbjct: 134 RGELARELAALTGDDGAFVSDGFGVVHRKQASVYDVARTLPAYAGGLVLAELEVLRTLTG 193 Query: 184 NPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKI 243 +PE+PY VVLGG+KVSDK+ VI L+ K DR+L+GG M FTFL A G VGSS +E D + Sbjct: 194 DPERPYAVVLGGSKVSDKLAVIEALLPKVDRLLVGGGMCFTFLAAQGHGVGSSLLESDMV 253 Query: 244 DLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIEL 303 + K LL +A +K +VLPVD V+A + + V GI +GWMGLDIGPET+ Sbjct: 254 ETCKRLLAEAGDK---LVLPVDVVVADAFAADADTRTVPA-TGIEDGWMGLDIGPETVAA 309 Query: 304 FKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKF 363 F + DA+T+ WNGPMGVFE+ FAEGT+ VA AIA E A +VVGGGDSAAAV Sbjct: 310 FGAAVRDARTLFWNGPMGVFEMAPFAEGTRGVATAIA---ESQAFSVVGGGDSAAAVRLL 366 Query: 364 GL-EDKFSHVSTGGGASLEFLEGKELPGIASIADKK 398 GL ED FSH+STGGGASLE+LEGKELPG+A +++++ Sbjct: 367 GLPEDGFSHISTGGGASLEYLEGKELPGVAVLSEER 402 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: 709 Number of extensions: 47 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: 402 Length adjustment: 35 Effective length of query: 619 Effective length of database: 367 Effective search space: 227173 Effective search space used: 227173 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