Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_012103714.1 CKL_RS16445 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000016505.1:WP_012103714.1 Length = 398 Score = 451 bits (1160), Expect = e-131 Identities = 221/398 (55%), Positives = 300/398 (75%), Gaps = 7/398 (1%) Query: 3 KMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGR 62 K TI DVD+KGKRV++R DFNVP+++G + D+ R+ +LPTIKY +E AKVIL SHLG+ Sbjct: 5 KKTIEDVDVKGKRVLVRCDFNVPLQEGKITDENRLIGSLPTIKYLMENNAKVILCSHLGK 64 Query: 63 PKGEPSPEFSLAPVAKRLSELLGKEVKFVPA--VVGDEVKKAVEELKEGEVLLLENTRFH 120 PKGE PE SL PVAKRLSELL KEV F VVG+ K AV+ +K+G+V+LL+NTR+ Sbjct: 65 PKGEVKPEMSLLPVAKRLSELLKKEVVFAADDNVVGENAKAAVKNMKDGDVILLQNTRYR 124 Query: 121 PGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPS-VAGFLMEKEIKFLS 179 ETKN +K ASL +I VNDAFGTAHRAH S VG+ +F+P+ V G+L++KE++FL Sbjct: 125 IEETKNQDNFSKELASLGEIFVNDAFGTAHRAHCSTVGVTKFLPTAVCGYLIQKELEFLG 184 Query: 180 KVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVE 239 NP +P+ +LGG KVSDKI VI NL+EK D ++IGG M +TF +A G +G+S VE Sbjct: 185 NAIENPSRPFTAILGGVKVSDKINVINNLLEKVDTLIIGGGMSYTFARAQGYTIGTSVVE 244 Query: 240 EDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPE 299 EDKI+ AKE+++KAKEKG++++LP+D V+ K + E ++ D I +G+MG+DIGP+ Sbjct: 245 EDKIEYAKEMIDKAKEKGIKLLLPIDRVVTDKFDESAE-PILEDDKNIKDGYMGMDIGPK 303 Query: 300 TIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAA 359 T +++ + D+KT++WNGPMGVFE +FA+GT VA A+A E GAIT++GGGDSAAA Sbjct: 304 TAKVYADAIKDSKTIIWNGPMGVFEFKNFAKGTFAVAKAMA---ESGAITIIGGGDSAAA 360 Query: 360 VNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADK 397 +N+ G DK +H+STGGGASLEFL G+ELPGI+++ +K Sbjct: 361 INQLGFGDKMTHISTGGGASLEFLGGEELPGISALNNK 398 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: 686 Number of extensions: 31 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: 398 Length adjustment: 34 Effective length of query: 620 Effective length of database: 364 Effective search space: 225680 Effective search space used: 225680 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