Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 17005 b2926 phosphoglycerate kinase (NCBI)
Query= BRENDA::P36204 (654 letters) >FitnessBrowser__Keio:17005 Length = 387 Score = 310 bits (793), Expect = 1e-88 Identities = 183/406 (45%), Positives = 257/406 (63%), Gaps = 27/406 (6%) Query: 1 MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60 M + + D+DL GKRV +R D NVPVKDG V D RIRA+LPTI+ AL+QGAKV++ SHL Sbjct: 1 MSVIKMTDLDLAGKRVFIRADLNVPVKDGKVTSDARIRASLPTIELALKQGAKVMVTSHL 60 Query: 61 GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119 GRP +GE + EFSL PV L + L V+ V + D V ++ EGE+++LEN RF Sbjct: 61 GRPTEGEYNEEFSLLPVVNYLKDKLSNPVRLVKDYL-DGV-----DVAEGELVVLENVRF 114 Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178 + GE K+D L+K +A+L D+ V DAFGTAHRA AS GI +F + AG L+ E+ L Sbjct: 115 NKGEKKDDETLSKKYAALCDVFVMDAFGTAHRAQASTHGIGKFADVACAGPLLAAELDAL 174 Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238 K P +P V ++GG+KVS K+ V+ +L + AD++++GG + TF+ A G +VG S Sbjct: 175 GKALKEPARPMVAIVGGSKVSTKLTVLDSLSKIADQLIVGGGIANTFIAAQGHDVGKSLY 234 Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIE---PGVEKKV--VRIDDGIPEGWMG 293 E D +D AK LL I +P D +A + P K V V+ D+ I Sbjct: 235 EADLVDEAKRLLTTC-----NIPVPSDVRVATEFSETAPATLKSVNDVKADEQI------ 283 Query: 294 LDIGPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGG 353 LDIG + + + L +AKT++WNGP+GVFE +F +GT+ VA AIA + A ++ GG Sbjct: 284 LDIGDASAQELAEILKNAKTILWNGPVGVFEFPNFRKGTEIVANAIA---DSEAFSIAGG 340 Query: 354 GDSAAAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADKKK 399 GD+ AA++ FG+ DK S++STGGGA LEF+EGK LP +A + ++ K Sbjct: 341 GDTLAAIDLFGIADKISYISTGGGAFLEFVEGKVLPAVAMLEERAK 386 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: 596 Number of extensions: 31 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: 387 Length adjustment: 34 Effective length of query: 620 Effective length of database: 353 Effective search space: 218860 Effective search space used: 218860 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 17 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