Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_039103171.1 FPB0191_RS00250 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Korea:Ga0059261_1644 (347 letters) >NCBI__GCF_000807275.1:WP_039103171.1 Length = 615 Score = 127 bits (319), Expect = 8e-34 Identities = 105/359 (29%), Positives = 172/359 (47%), Gaps = 35/359 (9%) Query: 14 MEREAAEAGAAVSRMLAANR---------DAIERVAARLRASPPAVVVTCARGSSDHAAT 64 ME+E E A+ L NR + +E A L +V C G++ HA Sbjct: 257 MEKEIFEQPIAIKNTLL-NRIKHGKVDLSELVEEHATVLAHVEHIQIVAC--GTAYHAGL 313 Query: 65 YAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLATVEHQRKAGA 124 A+Y E++TG+P ++ Y P N L + +SQSG++ D LA + + G Sbjct: 314 VARYWFESITGIP-CDVEIASEFRYRNPATRPNSLFITLSQSGETADTLAALRLAKTIGY 372 Query: 125 F-VVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAAWAQ------ 177 +A+ N S L AD+V+ KAG E VA+TK++ L + LVA ++Q Sbjct: 373 ISTLAICNVAASTLVREADLVLLTKAGTEVGVASTKAFTTQLTVLLLLVAKFSQIKNKPA 432 Query: 178 --DEALETAVADLPAQLERAFALDWSAAVTA--LTGASGLFVLGRGYGYGIAQEAALKFK 233 ++ + A+ LP ++E+ + A LGRG + IA E ALK K Sbjct: 433 LVEKQIVEALQILPNRIEQLLSSADKIEKLAKHFADKQHTLFLGRGDEFPIALEGALKLK 492 Query: 234 ETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAEFRSRGAEVLL-- 291 ET +HAE+++A E++HGP+A+V + V+ A+++ + ++ + E R+RG ++ + Sbjct: 493 ETSYIHAEAYAAGELKHGPLALVDKNMSVIVIAANNHLLDKLKSNIEEVRARGGQLYIFT 552 Query: 292 ---ADPAARQAGLPAIAAHPAIEPILIVQSFYK-----MANALALARGCDPDSPPHLNK 342 +D A + + A P IE L +Y +A +AL +G D D P +L K Sbjct: 553 SEDSDLADADSKNMHVIALPKIEE-LTASIYYTVPMQLLAYYVALIKGTDVDRPRNLAK 610 Lambda K H 0.317 0.128 0.360 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: 336 Number of extensions: 20 Number of successful extensions: 4 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: 347 Length of database: 615 Length adjustment: 33 Effective length of query: 314 Effective length of database: 582 Effective search space: 182748 Effective search space used: 182748 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 24 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