Align Fructose-bisphosphate aldolase; FBP aldolase; FBPA; EC 4.1.2.13; Fructose-1,6-bisphosphate aldolase (uncharacterized)
to candidate WP_084055816.1 B9A12_RS01770 hypothetical protein
Query= curated2:Q5XA12 (293 letters) >NCBI__GCF_900176285.1:WP_084055816.1 Length = 379 Score = 80.5 bits (197), Expect = 5e-20 Identities = 81/276 (29%), Positives = 121/276 (43%), Gaps = 22/276 (7%) Query: 3 IVSAEKFVQAARENGYAVGGFNTNNLEWTQAILRAAEAKQAPVLIQTSMGAAKYMGGYKV 62 +V+ + ++AA+++ + N + I+RA+ A APV+ + + Y Sbjct: 22 LVNGKALLKAAKKHKAMIMATNIRCRLPVEGIVRASMATGAPVMYEIARSELTYTEFTPA 81 Query: 63 C-QSLITNLVESMGIT-VPVAIHLDHGHYGDA----------LECIEVGYTSIMFDGSHL 110 I E +G T VP AIH DH E +E GYTS D SH+ Sbjct: 82 SFVDFIVKENERLGNTQVPFAIHGDHITVKSPEDKEPVAALIAEEMEAGYTSFAIDASHM 141 Query: 111 PVEENLAKTAEVVKIAHAKGVSVEAEVGTIGGEEDGIIGKGELAPIE-DAKAMVETGI-- 167 E NLA T+E+ + A G+S+E E+G IG + G + E + + E G+ Sbjct: 142 ENELNLAATSELARPIVAAGLSLEVELGEIGAKSGSAEGFTQPDEAEWFIRNLTEKGVHP 201 Query: 168 DFLAAGIGNIHGPY-PENWEGLALDHLEKLTAAVPGF--PIVLHGGSGIPDDQIKEAIRL 224 D LA G+IHG Y EG+ LD ++ A+ + I HG +G D+I I Sbjct: 202 DLLAINNGSIHGTYFGTAQEGIQLDLTLEIWKAIQPWEVDIAQHGITGTSLDKITSFINY 261 Query: 225 GVAKVNVNTESQIAFSNATREFARNYEANEAEYDGK 260 G+ K NV T + N FA N N + K Sbjct: 262 GIRKGNVGT----FWQNVAFGFAMNQNGNAITTEDK 293 Lambda K H 0.315 0.134 0.383 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: 238 Number of extensions: 13 Number of successful extensions: 2 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: 293 Length of database: 379 Length adjustment: 28 Effective length of query: 265 Effective length of database: 351 Effective search space: 93015 Effective search space used: 93015 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: 42 (22.0 bits) S2: 49 (23.5 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