Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_028485251.1 A377_RS0103985 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000384235.1:WP_028485251.1 Length = 393 Score = 334 bits (857), Expect = 4e-96 Identities = 179/393 (45%), Positives = 261/393 (66%), Gaps = 11/393 (2%) Query: 1 MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60 M + + D+DL GKRV++R D NVPVK+G V D RIRA+LPT+K A E GAKV+++SHL Sbjct: 1 MSVLKMSDLDLAGKRVLIREDLNVPVKNGKVTSDARIRASLPTMKMAAEAGAKVMIMSHL 60 Query: 61 GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119 GRP +GE E S+APVA LSE LGK+V+ + + +V ++ GE++LLEN RF Sbjct: 61 GRPTEGEFDQESSMAPVAADLSEKLGKDVRLIKDYLDGDV-----DVAAGEIVLLENVRF 115 Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178 + GE KND L+K +A+L DI+V DAFGTAHRA AS G ++ P + AG L+ E++ L Sbjct: 116 NVGEKKNDVALSKKYAALCDIYVMDAFGTAHRAQASTHGAGEYAPVACAGPLLAAELEAL 175 Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238 K + P++P V ++GG+KVS K+ V+ +L EK D++++GG + TF++A G VG+S Sbjct: 176 GKALHEPKRPMVAIVGGSKVSTKLTVLESLSEKVDQLVVGGGIANTFIEAAGHNVGNSLS 235 Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298 E D + K+L E + +G I L D V ++ + + + + + + M DIGP Sbjct: 236 ETDLVPTCKKLNEIMESRGAAIPLASDVVCGKEFSENAKAETKPVAEVVDDD-MIFDIGP 294 Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358 ++ + + +A TVVWNGP+GVFE D F EGTK +++AIA E A ++ GGGD+ A Sbjct: 295 DSAAELAKIIKEAGTVVWNGPVGVFEFDQFGEGTKAISMAIA---ESDAFSIAGGGDTLA 351 Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGI 391 A++K+ + DK S++STGGGA LEFLEGK+LP + Sbjct: 352 AIDKYDIADKVSYISTGGGAFLEFLEGKKLPAV 384 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: 596 Number of extensions: 40 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: 393 Length adjustment: 34 Effective length of query: 620 Effective length of database: 359 Effective search space: 222580 Effective search space used: 222580 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