Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate Ac3H11_4404 Phosphoglycerate kinase (EC 2.7.2.3)
Query= BRENDA::P36204 (654 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4404 Length = 399 Score = 313 bits (803), Expect = 7e-90 Identities = 177/381 (46%), Positives = 244/381 (64%), Gaps = 13/381 (3%) Query: 12 KGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP-KGEPSP 69 +G+RV +R D NVP D G + +DTRIRA++P I+ AL+ GA V++ SHLGRP +GE P Sbjct: 16 QGQRVFIRADMNVPQDDAGQITEDTRIRASIPCIRMALDAGAAVMVTSHLGRPTEGEFKP 75 Query: 70 EFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDPE 129 E SLAPVA+RLSELLG++V V V D V A G+V+LLEN R + GE KN E Sbjct: 76 EDSLAPVAQRLSELLGRDVPLVANWV-DGVTVA-----PGQVVLLENCRLNVGEKKNKDE 129 Query: 130 LAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKVTYNPEKP 188 LA+ A+L DI VNDAFGTAHRA + GIAQF P + AG L+ EI L+K P++P Sbjct: 130 LARKLAALCDIFVNDAFGTAHRAEGTTYGIAQFAPVACAGPLLSAEIDALTKALAQPQRP 189 Query: 189 YVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDLAKE 248 ++ G+KVS K+ ++ +L +K D++++GG + TF+ A G +G S E D +D AK Sbjct: 190 LAAIVAGSKVSTKLTILQSLADKVDQLIVGGGIANTFMLAAGLPIGKSLAEPDLLDAAKS 249 Query: 249 LLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFKQKL 308 ++ K +G E+ +P D V+A+ V D P+ + LDIGP+T +L Sbjct: 250 VMAAMKARGAEVPIPTDVVVAKAFAADAPATVKAATDVAPDDLI-LDIGPDTAARLAAQL 308 Query: 309 SDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKFGLEDK 368 A T+VWNGP+GVFE F GT+ +A AIA E A ++ GGGD+ AA+ K+G+E + Sbjct: 309 KSAGTIVWNGPVGVFEFAAFENGTRALAAAIA---ESPAFSIAGGGDTLAAIAKYGIEKQ 365 Query: 369 FSHVSTGGGASLEFLEGKELP 389 ++STGGGA LE LEGK+LP Sbjct: 366 VGYISTGGGAFLEVLEGKKLP 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: 561 Number of extensions: 23 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: 399 Length adjustment: 34 Effective length of query: 620 Effective length of database: 365 Effective search space: 226300 Effective search space used: 226300 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