Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_074201709.1 BUQ81_RS07240 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_900141795.1:WP_074201709.1 Length = 400 Score = 341 bits (875), Expect = 3e-98 Identities = 186/389 (47%), Positives = 257/389 (66%), Gaps = 11/389 (2%) Query: 11 LKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP-KGEPSP 69 L GKRV++R D NVPVKDG V D RI A+LPTIK A++ GAKV+L+SHLGRP +GE Sbjct: 15 LAGKRVLIREDLNVPVKDGKVTSDKRIVASLPTIKMAMDAGAKVMLMSHLGRPTEGEYDE 74 Query: 70 EFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDPE 129 ++SLAPVA LSE LG+EV + + V E+ EGEV+LLEN RF+ GE KND Sbjct: 75 QYSLAPVAADLSEKLGREVPLIKDYLDGNV-----EVGEGEVVLLENVRFNVGEKKNDEA 129 Query: 130 LAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKVTYNPEKP 188 LAK +A+L D+ V DAFGTAHRA AS G+ + P + AG L+ E++ L K NP++P Sbjct: 130 LAKKYAALCDVFVMDAFGTAHRAQASTYGVGVYAPIAAAGPLLAAELEALGKALENPDRP 189 Query: 189 YVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDLAKE 248 V ++GG+KVS K+ V+ +L EK D++++GG + TF+ A G VG S E D I AK Sbjct: 190 MVAIVGGSKVSTKLTVLESLAEKVDQLVVGGGIANTFIAAAGYNVGKSLYEPDLIPTAKR 249 Query: 249 LLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFKQKL 308 L+E + +G + + D V+A+ E + ++D+ + + M DIGPE+ + + Sbjct: 250 LMETMEARGAGVPIAKDVVVAKAFAEDAEATLKKVDE-VADDDMIFDIGPESAKELADII 308 Query: 309 SDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKFGLEDK 368 A TVVWNGP+GVFE D F +GT+ +A AIAA A ++ GGGD+ AA++K+G+ED Sbjct: 309 MQAGTVVWNGPVGVFEFDQFGKGTETIAKAIAA---SKAFSIAGGGDTLAAIDKYGVEDG 365 Query: 369 FSHVSTGGGASLEFLEGKELPGIASIADK 397 S++STGGGA LEFLEGK+LP + + K Sbjct: 366 VSYISTGGGAFLEFLEGKKLPAVEMLEKK 394 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: 662 Number of extensions: 35 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: 400 Length adjustment: 34 Effective length of query: 620 Effective length of database: 366 Effective search space: 226920 Effective search space used: 226920 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