Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_046010654.1 OLEAN_RS19710 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Korea:Ga0059261_1644 (347 letters) >NCBI__GCF_000967895.1:WP_046010654.1 Length = 613 Score = 132 bits (332), Expect = 2e-35 Identities = 104/319 (32%), Positives = 157/319 (49%), Gaps = 39/319 (12%) Query: 51 VVTCARGSSDHAATYAKYLIETLTGVPTASAALSVAS--LYDAPVAPGNGLCLAISQSGK 108 ++ C G+S H+ KY IE G+P + VAS Y V N L + ISQSG+ Sbjct: 302 IIAC--GTSYHSGMVTKYWIEKYAGIP---CQVEVASEFRYRHTVIAKNTLLITISQSGE 356 Query: 109 SPDLLATVEHQRKAGAFV-VAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAA 167 + D LA + ++ G + + N S L +D+ + AGPE VA+TK++ L A Sbjct: 357 TADTLAALRKAKEQGLLASMTVCNVPGSSLVRESDLCLMTNAGPEIGVASTKAFTTQLTA 416 Query: 168 IAALVAAWAQ----DEALET----AVADLPAQLERAFALDWSAAVTALTGASGLFV---- 215 + L A A+ EA ET A+ LP +E+A ALD + S LF Sbjct: 417 LLLLTVALAKRNGMSEAAETEIVTALHQLPGLVEKALALD-----PVIEKISQLFADKHH 471 Query: 216 ---LGRGYGYGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAG 272 LGRG Y IAQE ALK KE +HAE++ A E++HGP+A+V E ++A A + Sbjct: 472 SLFLGRGPMYPIAQEGALKLKEISYIHAEAYPAGELKHGPLALVDEDMPIIAVAPKNDLL 531 Query: 273 ESVRETVAEFRSRGAEV-LLADPAA--------RQAGLPAIAAHPAIEPILIVQSFYKMA 323 E + + E ++RG E+ + AD + LP + +EPI+ + ++ Sbjct: 532 EKLVSNLEEVKARGGELFVFADESVNLYDLDDQHLVSLPTVPC--CLEPIVYIIPLQLLS 589 Query: 324 NALALARGCDPDSPPHLNK 342 +A+ +G D D P +L K Sbjct: 590 YHVAVLKGTDVDQPRNLAK 608 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: 348 Number of extensions: 18 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: 347 Length of database: 613 Length adjustment: 33 Effective length of query: 314 Effective length of database: 580 Effective search space: 182120 Effective search space used: 182120 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