Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_010961266.1 MCA_RS09890 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000008325.1:WP_010961266.1 Length = 391 Score = 358 bits (919), Expect = e-103 Identities = 192/392 (48%), Positives = 267/392 (68%), Gaps = 12/392 (3%) Query: 8 DVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP-KGE 66 D+DL GKRV++R DFNVPVKDG V D RIRAALPTI++AL+ GA V+L+SHLGRP +GE Sbjct: 8 DIDLAGKRVLIREDFNVPVKDGRVTSDARIRAALPTIRHALDAGAAVMLMSHLGRPTEGE 67 Query: 67 PSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKN 126 + EFS+ PVA RLSELLG+ V V +G + G V+L EN RF+ GE K+ Sbjct: 68 YAEEFSMKPVADRLSELLGQPVTLVKDYLGGA------DPAVGSVVLFENVRFNKGEKKD 121 Query: 127 DPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSV-AGFLMEKEIKFLSKVTYNP 185 D LA+ A+L D++V DAFGTAHRA AS G+ ++ P+ AG L+ E+ L + ++P Sbjct: 122 DEVLARQLAALCDVYVMDAFGTAHRAEASTHGVGKYAPTACAGLLLATELDALGRALHDP 181 Query: 186 EKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDL 245 +P V ++GG+KVS K+ V+ +L + D++++GG + TF+KA G VG S EED + Sbjct: 182 ARPLVAIVGGSKVSTKLTVLDSLSQVVDQLIVGGGIANTFIKAAGFNVGKSLYEEDLVAE 241 Query: 246 AKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFK 305 A+ L+E AK KG EI +PVD V+ ++ + E +V+ I E M LDIGPET + Sbjct: 242 ARRLMEAAKAKGGEIPVPVDVVVGKRFD-AAEPAMVKSVADIAEDDMILDIGPETSRRYA 300 Query: 306 QKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKFGL 365 + + A TVVWNGP+GVFE D F EGT+++ LAIA E A ++ GGGD+ AA++K+G+ Sbjct: 301 EFIGRAGTVVWNGPVGVFEFDQFGEGTRRLGLAIA---ESHAFSIAGGGDTLAAIDKYGI 357 Query: 366 EDKFSHVSTGGGASLEFLEGKELPGIASIADK 397 D+ S++STGGGA LEFLEGK+LP +A + + Sbjct: 358 ADRISYISTGGGAFLEFLEGKQLPAVAMLESR 389 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: 627 Number of extensions: 45 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