Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate CA265_RS19160 CA265_RS19160 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::ANA3:7025965 (332 letters) >FitnessBrowser__Pedo557:CA265_RS19160 Length = 612 Score = 131 bits (330), Expect = 4e-35 Identities = 96/329 (29%), Positives = 162/329 (49%), Gaps = 36/329 (10%) Query: 28 MQQLGEKLRAFDPRFVMIVGRGSSDHAGVFAKYLFEIEAGVPTFAAAPSVASVYGKTLKL 87 +++ EKL+ D ++IV G+S HAG+ +YL E A +P S Y + Sbjct: 286 IKEFAEKLKNIDR--IIIVACGTSWHAGLVGEYLIEEYARIPVEVEYASEFR-YRNPIIT 342 Query: 88 EGGLVIVISQSGRSPDILAQARMAKNAGAFCVALVNDETAPIKDIVDVVVPLRAGEEKAV 147 E +VI ISQSG + D +A MAK GA + N A I + V AG E V Sbjct: 343 EKDVVIAISQSGETADTMAAIEMAKERGATIFGICNVAGASIPRLTHAGVYTHAGPEIGV 402 Query: 148 AATKSYLATLSAILQLASAWTQSES---------LAAAVNSLPQALQTAVDAEPQLTPAS 198 A+TK++ A ++ + +A Q + L ++++P+ +Q A+++ + + Sbjct: 403 ASTKAFTAQVTVLTLMAFYMAQQKGTITTSKLIELLTELDNIPEKIQVALESNDLIKEVA 462 Query: 199 --VENVKNLVVLGRGLGYAVSKEIALKLKEVCSIHAEAFSSAEFLHGPVTLVEKKLTIVD 256 +++ N + LGRG G+ V+ E ALKLKE+ IHAE + +AE HGP+ L+++++ +V Sbjct: 463 EKIKDSTNCLFLGRGSGFPVALEGALKLKEISYIHAEGYPAAEMKHGPIALIDEEMPVVF 522 Query: 257 VCIGDESYASHIEQIENV-SQRGADLVHLNQTSTDIH-----------------PRVAPL 298 + + SY I I+ V +++G + + Q T++ P +A + Sbjct: 523 IATQNSSYEKVISNIQEVKARKGKVIAIVTQGDTEVKKMADYCIEIPDANEAFLPLIATI 582 Query: 299 ALLQRFYIDVAAVAIARGIDPDQPAGLKK 327 L Y +A+ RG + DQP L K Sbjct: 583 PLQLLSY----HIAVMRGCNVDQPRNLAK 607 Lambda K H 0.316 0.130 0.357 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: 418 Number of extensions: 17 Number of successful extensions: 3 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: 332 Length of database: 612 Length adjustment: 33 Effective length of query: 299 Effective length of database: 579 Effective search space: 173121 Effective search space used: 173121 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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