Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_058932522.1 AU252_RS22005 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_001484605.1:WP_058932522.1 Length = 408 Score = 338 bits (866), Expect = 4e-97 Identities = 187/399 (46%), Positives = 256/399 (64%), Gaps = 16/399 (4%) Query: 11 LKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPSPE 70 ++G+ +++R D NVP+ V DD RI+A+LP + + GA+V++ +HLGRPKG P + Sbjct: 14 VRGRYILVRSDLNVPLDGSTVTDDGRIKASLPVLGKLTDAGARVLVTAHLGRPKGAPEEK 73 Query: 71 FSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET-KNDPE 129 +SL P RL+EL +V VG K+ L++GEVL+LEN RF ET K+D E Sbjct: 74 YSLRPAVARLAELAAFKVSLAQDTVGGSAKELAASLQDGEVLVLENVRFDARETSKDDAE 133 Query: 130 LAKFWASLADI------HVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTY 183 F L + +V+DAFG HR HAS +A +PS G L+ E++ L K+T Sbjct: 134 RGTFADELVALTGANGAYVDDAFGAVHRKHASVYDVATRLPSYQGDLVHTEVEVLRKLTA 193 Query: 184 NPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKI 243 + ++PYVVVLGG+KVSDK+ VI NL+ KAD IL+GG M+FTFL A G V S +EED+I Sbjct: 194 DTQRPYVVVLGGSKVSDKLAVIDNLIGKADTILVGGGMLFTFLAAEGHSVAGSLLEEDQI 253 Query: 244 DLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRID--DGIPEG--WMGLDIGPE 299 + ++ L++A G E ++P D V+A K + + V D +G G +GLDIGP+ Sbjct: 254 PVVQDYLKRAAGAGTEFIVPTDVVVAGKFAADADYETVPADGIEGSSFGAQGIGLDIGPD 313 Query: 300 TIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAA 359 + F ++ AKTV WNGPMGVFE + F+ GT+ VA ALTE A TVVGGGDSAAA Sbjct: 314 SAAAFADRIKGAKTVFWNGPMGVFEFEAFSGGTRAVA---QALTEVDAFTVVGGGDSAAA 370 Query: 360 VNKFGL-EDKFSHVSTGGGASLEFLEGKELPGIASIADK 397 V G +D+F H+STGGGASLE+LEGKELPG+ S+ D+ Sbjct: 371 VRTLGFADDQFGHISTGGGASLEYLEGKELPGL-SVLDR 408 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: 680 Number of extensions: 38 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 10 2024. The underlying query database was built on Apr 09 2024.
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