Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_013459152.1 SULKU_RS01475 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000183725.1:WP_013459152.1 Length = 396 Score = 397 bits (1020), Expect = e-115 Identities = 199/395 (50%), Positives = 279/395 (70%), Gaps = 8/395 (2%) Query: 1 MEKMTIRDVDLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSH 59 M+ + I++ D+ GK+V +R DFNVP+ D G + DD RIR+AL TI Y L+Q +IL SH Sbjct: 1 MQLLGIKECDIHGKKVFIRCDFNVPMDDYGNITDDRRIRSALATINYCLDQKCAIILASH 60 Query: 60 LGRPKGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119 GRPKGEP ++SLAP+A+RL +LL +V+ VVG+ K ELK GEVLLLEN RF Sbjct: 61 FGRPKGEPDEKYSLAPIARRLHQLLKIDVQVADDVVGESALKLAHELKNGEVLLLENLRF 120 Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPS---VAGFLMEKEIK 176 GETKNDP+L+ AS+A++++NDAFG +HRAHAS GI + AGFL++KEI+ Sbjct: 121 EKGETKNDPDLSAALASMAEVYINDAFGVSHRAHASVEGITAHFDNAHKAAGFLLQKEIQ 180 Query: 177 FLSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSS 236 F + +P +P+ ++GG+KVS K+ + NL+ K D++LIGG M FTFLKALG +VG+S Sbjct: 181 FFGTLLEHPVRPFAAIVGGSKVSGKLEALINLLPKVDKMLIGGGMAFTFLKALGHDVGNS 240 Query: 237 RVEEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDI 296 VE+D I A +++E+AK GV+ LPVD V A+K P ++ + + IP GWMGLDI Sbjct: 241 LVEDDLIPEALKIMEEAKRLGVKFYLPVDVVAAEKFAPDSASRLCSVQE-IPSGWMGLDI 299 Query: 297 GPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDS 356 GP T+ L++Q L D +T++WNGPMGV+E+D +A G+ ++A +A + A +VVGGGD+ Sbjct: 300 GPATVRLYRQVLGDVQTILWNGPMGVYEMDRYARGSNKIAHFVA---DSYATSVVGGGDT 356 Query: 357 AAAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGI 391 A V + GL+++ + +STGGGASLE LEGK LPG+ Sbjct: 357 ADLVQRVGLDEEITFISTGGGASLELLEGKILPGV 391 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: 34 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: 396 Length adjustment: 34 Effective length of query: 620 Effective length of database: 362 Effective search space: 224440 Effective search space used: 224440 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