Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_013645964.1 METBO_RS11885 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000191585.1:WP_013645964.1 Length = 408 Score = 231 bits (588), Expect = 6e-65 Identities = 154/407 (37%), Positives = 220/407 (54%), Gaps = 26/407 (6%) Query: 5 TIRDVDLKGKRVIMRVDFNVPV--KDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGR 62 TI D DL K V++RVD N PV G++ DDTRI+ TI ++GAK ++L+H R Sbjct: 7 TIDDFDLDDKTVLVRVDINSPVDPSSGLILDDTRIKLHAETIAELSKKGAKTVVLAHQSR 66 Query: 63 PKGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPG 122 P + +L A LS +L EV +V + G + A+ ++K G++LLLEN RF+ Sbjct: 67 PGKKDFT--TLEQHADALSNILKHEVAYVDDIFGSHARNAIGKMKRGDILLLENVRFYSE 124 Query: 123 ET-KNDPEL------AKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEI 175 E K DP+L + A +AD VNDAF AHR+ S VG A +PS AG +ME+E+ Sbjct: 125 EILKRDPKLQSETHMVQNLAPMADYFVNDAFAAAHRSQPSLVGFAFALPSAAGRIMEREL 184 Query: 176 KFLSKVTYNPEKPYVVVLGGAKVSDKIGVITNLME--KADRILIGGAMMFTFLKALGKEV 233 K L N +KP + VLGG KV D I V+ N++E AD IL G + FL G + Sbjct: 185 KALYNAMNNVQKPCIYVLGGVKVDDSIMVMENVLENGSADYILTTGLVANIFLWGSGVNI 244 Query: 234 GSSRVE----EDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPE 289 E + D ++ + K G +I+LP D + +K+V + +P Sbjct: 245 RKYNKEFIEKKGYCDFVRKSKKLLKNFGDQIILPKDLAVCMG-----DKRVEFSVEDLPN 299 Query: 290 GWMGLDIGPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAIT 349 + DIG ETI+ + + A T+ NGP GVFE DDF GT + AIA+ + Sbjct: 300 QPI-FDIGTETIKEYAGYIRRANTLFANGPAGVFEKDDFNIGTDDILNAIAS---SPGFS 355 Query: 350 VVGGGDSAAAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIAD 396 ++GGG AAA N+ GL SH+S+GGGAS+ L G++LP + + D Sbjct: 356 IIGGGHLAAAANQMGLSKGISHISSGGGASINLLAGEDLPVVTVLRD 402 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: 600 Number of extensions: 37 Number of successful extensions: 5 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: 408 Length adjustment: 35 Effective length of query: 619 Effective length of database: 373 Effective search space: 230887 Effective search space used: 230887 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