Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate Echvi_1524 Echvi_1524 glucosamine--fructose-6-phosphate aminotransferase (isomerizing)
Query= reanno::Korea:Ga0059261_1644 (347 letters) >FitnessBrowser__Cola:Echvi_1524 Length = 613 Score = 135 bits (340), Expect = 3e-36 Identities = 95/310 (30%), Positives = 152/310 (49%), Gaps = 19/310 (6%) Query: 51 VVTCARGSSDHAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSP 110 ++ A G+S HA A+YL E VP S Y PV +AISQSG++ Sbjct: 300 IIITACGTSWHAGLVAEYLFEEFARVPVEVEYASEFR-YRNPVINSRDFVIAISQSGETA 358 Query: 111 DLLATVEHQRKAGAFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIA- 169 D LA +E ++ GA + + N S +A AGPE VA+TK++ ++ ++ Sbjct: 359 DTLAAIELAKQKGATIFGVCNVVGSSIARATHAGSYTHAGPEIGVASTKAFTAQISVLSM 418 Query: 170 -ALVAAWAQDEALETAVADL-------PAQLERAFALDWSAAVTALT--GASGLFVLGRG 219 AL+ + + E+ +L PA++E+A L+ A A LGRG Sbjct: 419 MALMLGYQRGTLPESKYMELLSELEAIPAKVEKALKLNEQIERIAAQYKDARNFLYLGRG 478 Query: 220 YGYGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETV 279 Y + +A E ALK KE +HAE + AAE++HGP+A++ E V+ A+ D + E V + Sbjct: 479 YNFPVALEGALKLKEISYIHAEGYPAAEMKHGPIALIDEEMPVVFIATQDSSYEKVVSNI 538 Query: 280 AEFRSRGAEVLL----ADPAARQAGLPAI---AAHPAIEPILIVQSFYKMANALALARGC 332 E ++R +++ D R+ I AH A P++ V +++ +A+ RGC Sbjct: 539 QEVKARKGKIIAVVTEGDQTVRKMADHVIEIPRAHEAFVPLISVLPLQQLSYHIAVMRGC 598 Query: 333 DPDSPPHLNK 342 + D P +L K Sbjct: 599 NVDQPRNLAK 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: 372 Number of extensions: 19 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: 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 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