Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_104912972.1 C3B54_RS01720 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Korea:Ga0059261_1644 (347 letters) >NCBI__GCF_002950575.1:WP_104912972.1 Length = 615 Score = 129 bits (324), Expect = 2e-34 Identities = 108/352 (30%), Positives = 161/352 (45%), Gaps = 23/352 (6%) Query: 13 LMEREAAEAGAAVSRMLAANRDAIERVAARLRASPPAVVVTCARGSSDHAATYAKYLIET 72 + E+ A A SR+ I +A + + VV A G++ ++A Y +E Sbjct: 260 ISEQPEAVANTLRSRITPEGHIDIPELAKVVADTQITRVVFIACGTAAYSAMLGAYAMEK 319 Query: 73 LTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLATVEHQRKAGAFVVAMVNA 132 +P AS LS Y V + L +++SQSG++ D L V H +AGA V++ N Sbjct: 320 WAHIP-ASVELSHEFRYRDAVIDAHTLVVSVSQSGETMDTLMAVRHAAEAGATTVSICNT 378 Query: 133 EDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAAWAQD-------EALETAV 185 + + + + + AGPE +VA+TK++ + A L A+ + E E A Sbjct: 379 QGATIPRESTATLYTHAGPEVAVASTKAFSAQVVATYLLALAFGEARGALSAAERAELAE 438 Query: 186 ADLPAQLERAFALDWSAAVTALT----GASGLFVLGRGYGYGIAQEAALKFKETCALHAE 241 A L A + A + + L + LGR GY IA E ALK KE +HAE Sbjct: 439 ALLAAPDQMAEMVQTGERIHELAHWMADTHSVLYLGRHVGYPIALEGALKLKELAYIHAE 498 Query: 242 SFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVA----EFRSRGAEVLLADPAAR 297 F+A E++HGP+A++ V S R S+ V E R+RGA V+ Sbjct: 499 GFAAGELKHGPIALIEPGQIVFVVVPSPRDPRSLHSKVVSNIQEIRARGARVIALAERGD 558 Query: 298 QAGLP----AIA---AHPAIEPILIVQSFYKMANALALARGCDPDSPPHLNK 342 A LP IA AH +EP+L V + LA+A+G D D P +L K Sbjct: 559 AAVLPFADEVIALPPAHTFVEPLLAVIPLHLFGMELAMAKGLDVDQPRNLAK 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: 418 Number of extensions: 21 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: 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