Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate GFF2967 HP15_2911 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >FitnessBrowser__Marino:GFF2967 Length = 386 Score = 343 bits (879), Expect = 1e-98 Identities = 195/399 (48%), Positives = 266/399 (66%), Gaps = 19/399 (4%) Query: 1 MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60 +++MT D++L GKRV++R D NVPVKDG V D RIRA+LPTIK A + GAKV+L+SHL Sbjct: 3 IKRMT--DLNLAGKRVLIREDLNVPVKDGKVSSDARIRASLPTIKAAKDAGAKVMLMSHL 60 Query: 61 GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119 GRP +G S+ PVA L+++LG+EV+ + + D V E+ +GEV+L EN RF Sbjct: 61 GRPEEGVYDEASSMKPVADHLTKVLGQEVRLIKDYL-DGV-----EVADGEVVLFENVRF 114 Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178 + GE K++ +LAK +A+L D++V DAFGTAHRA AS G+A+F P + AG L+ E++ L Sbjct: 115 NKGEKKDNEDLAKKYAALCDVYVMDAFGTAHRAQASTHGVARFAPEACAGPLLAAELEAL 174 Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238 K NP KP V ++GG+KVS K+ V+ L + D I++GG + TFL A G VG S Sbjct: 175 GKALDNPAKPVVAIVGGSKVSTKLDVLNALEKVCDSIIVGGGIANTFLAAAGHPVGKSLC 234 Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298 E D ID AKE+ + VEI LPVD V+A + V I D + E M LD+GP Sbjct: 235 EHDLIDTAKEIASR-----VEIPLPVDVVVASEFAETATATVKNISD-VTEDDMILDVGP 288 Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358 ET F + L +AKT++WNGP+GVFE D F GTK +A AIA E A ++ GGGD+ A Sbjct: 289 ETAGEFAELLKNAKTILWNGPVGVFEFDQFGNGTKALAEAIA---ESDAFSLAGGGDTVA 345 Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADK 397 AV+K+G+ DK S++STGGGA LEF+EGK LP +A + ++ Sbjct: 346 AVDKYGVADKISYISTGGGAFLEFVEGKTLPAVAVLEER 384 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: 619 Number of extensions: 38 Number of successful extensions: 7 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: 386 Length adjustment: 34 Effective length of query: 620 Effective length of database: 352 Effective search space: 218240 Effective search space used: 218240 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 09 2024. 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