Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_041097216.1 SUTH_RS03805 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000828635.1:WP_041097216.1 Length = 393 Score = 326 bits (835), Expect = 1e-93 Identities = 183/396 (46%), Positives = 254/396 (64%), Gaps = 11/396 (2%) Query: 6 IRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK- 64 + D DL GKRV +R D NVPVKDG V D RI A++PTI++ L+ GAKV++ SHLGRP+ Sbjct: 6 LTDFDLAGKRVFIRADLNVPVKDGKVTSDARITASMPTIQHCLKAGAKVMVTSHLGRPEE 65 Query: 65 GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124 G + E SL PVA ++ LGK V+ V+ D V E + GEV+LLEN RF+ GE Sbjct: 66 GVYADENSLKPVADVMAAQLGKPVR----VIRDWVDGGFE-VAAGEVVLLENCRFNKGEK 120 Query: 125 KNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSV-AGFLMEKEIKFLSKVTY 183 KN AK +A+L D+ V DAFGTAHRA AS G+AQF P+ AG L+ +E++ L+K Sbjct: 121 KNVEATAKKYAALCDLFVMDAFGTAHRAEASTYGVAQFAPAACAGLLVAEELEALTKALA 180 Query: 184 NPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKI 243 P +P V ++GG+KVS K+ V+ L EK D++++GG + TFLKA G+ VG S E+D + Sbjct: 181 TPARPMVAIVGGSKVSTKLTVLEALSEKVDQMVVGGGIANTFLKATGRNVGKSLCEDDLV 240 Query: 244 DLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIEL 303 A+ L++K +G I + VD V +K + E V + + + M DIGP++ + Sbjct: 241 PTAQALMKKMTARGATIPIAVDVVCGKKFD-AAEPAVAKDAGAVADDDMIFDIGPKSAQE 299 Query: 304 FKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKF 363 + A TVVWNGP+GVFE D F EGTK +A+AIA + A T+ GGGD+ AA+ K+ Sbjct: 300 LVDIIMKAGTVVWNGPVGVFEFDQFGEGTKAIAMAIA---KTKAFTLAGGGDTIAAIQKY 356 Query: 364 GLEDKFSHVSTGGGASLEFLEGKELPGIASIADKKK 399 + DK S++ST GGA LEFLEGK+LP + + + K Sbjct: 357 DIYDKVSYISTAGGAFLEFLEGKKLPAVDMLEQRAK 392 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: 586 Number of extensions: 38 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: 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