Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_025329981.1 SALWKB2_RS01810 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000600005.1:WP_025329981.1 Length = 391 Score = 355 bits (912), Expect = e-102 Identities = 183/391 (46%), Positives = 267/391 (68%), Gaps = 11/391 (2%) Query: 6 IRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK- 64 + D D+ GK V++RVD NVP+KDGV+ DDTRIRA+L +I++ L+QGA V++L+HLGRPK Sbjct: 6 LADQDVSGKTVVIRVDMNVPIKDGVIVDDTRIRASLASIRFCLQQGAAVVVLTHLGRPKA 65 Query: 65 GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124 G P PE S+APVA+RL ELLG+ V V ++ ++ +L+ G V++L N R + GE Sbjct: 66 GAPKPEDSVAPVAQRLGELLGQNVS-----VAEDWREHKPQLQAGHVIMLPNVRLNIGEK 120 Query: 125 KNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKVTY 183 +ND LA +A+L DI+VNDAFGTAHRA AS +A+F P + AG L+ E++ L+ Sbjct: 121 ENDQALAAAYAALGDIYVNDAFGTAHRAEASTAAVAEFAPLACAGMLLTAELEALTHAVQ 180 Query: 184 NPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKI 243 NP+ P V ++GG+KVS K+ ++ +L +K D +++GG + TFL A G VG S E D + Sbjct: 181 NPQAPVVAIVGGSKVSTKLTILESLADKVDHLIVGGGIANTFLLAKGLPVGQSLAEADLV 240 Query: 244 DLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIEL 303 D A++++ K KG +I LPVD V+A++ ++ + D + E M LDIGP++ + Sbjct: 241 DSARQIMAKIAAKGGDIPLPVDVVVAKRFAADAAAEIKNVAD-VAEDDMILDIGPQSAQR 299 Query: 304 FKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKF 363 + + +AKT+VWNGP+GVFE FA GTK +A AIA + A ++ GGGD+ AA+ +F Sbjct: 300 LAEMMKEAKTIVWNGPVGVFEFAAFAHGTKVLAKAIA---DSDAYSIAGGGDTLAAIAQF 356 Query: 364 GLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 G+ D S++STGGGA LEFLEGK LP +A++ Sbjct: 357 GITDDISYISTGGGAFLEFLEGKTLPAVAAL 387 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: 603 Number of extensions: 32 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: 391 Length adjustment: 34 Effective length of query: 620 Effective length of database: 357 Effective search space: 221340 Effective search space used: 221340 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