Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate Ac3H11_3072 Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] (EC 2.6.1.16)
Query= reanno::Korea:Ga0059261_1644 (347 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3072 Length = 641 Score = 122 bits (305), Expect = 3e-32 Identities = 101/316 (31%), Positives = 151/316 (47%), Gaps = 30/316 (9%) Query: 51 VVTCARGSSDHAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNG--LCLAISQSGK 108 V+ A G+S ++ AKY +E + G+PT + VAS Y + N L + I+QSG+ Sbjct: 327 VLILACGTSYYSGCAAKYWLEEIAGIPTQ---VEVASEYRYRTSVPNPRTLVVTITQSGE 383 Query: 109 SPDLLATVEHQRKAGA-FVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAA 167 + D LA + H + G + + N S + + +AG E VA+TK++ LA Sbjct: 384 TADTLAALRHAQSLGMQHTLTICNVVTSAMVRECKLAYITRAGVEIGVASTKAFTTQLAG 443 Query: 168 IAALVAAWAQDE---------ALETAVADLPAQLERAFALD-----WSAAVTALTGASGL 213 + L A AQ + A A+ LP L+ AL+ W+ + A Sbjct: 444 LFLLTLALAQSKGRLSEEQEAAHLKAMRHLPVALQAVLALEPQLISWAEDFARMENA--- 500 Query: 214 FVLGRGYGYGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGE 273 LGRG Y IA E ALK KE +HAE++ A E++HGP+A+V A V+ A +D E Sbjct: 501 LFLGRGLHYPIALEGALKLKEISYIHAEAYPAGELKHGPLALVTSAMPVVTVAPNDALLE 560 Query: 274 SVRETVAEFRSR-GAEVLLADPAAR---QAGLPAIAA---HPAIEPILIVQSFYKMANAL 326 ++ + E R+R G +LAD G+ I + A+ P+L V +A Sbjct: 561 KLKSNMQEVRARAGVLYVLADGDTHIESSEGIHVIRMPEHYGALSPLLHVVPLQLLAYHT 620 Query: 327 ALARGCDPDSPPHLNK 342 A ARG D D P +L K Sbjct: 621 ACARGTDVDKPRNLAK 636 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: 431 Number of extensions: 27 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: 641 Length adjustment: 33 Effective length of query: 314 Effective length of database: 608 Effective search space: 190912 Effective search space used: 190912 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