Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_040534573.1 L248_RS03250 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Korea:Ga0059261_1644 (347 letters) >NCBI__GCF_000469325.1:WP_040534573.1 Length = 604 Score = 119 bits (298), Expect = 2e-31 Identities = 97/307 (31%), Positives = 143/307 (46%), Gaps = 25/307 (8%) Query: 55 ARGSSDHAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLA 114 A G+S HA L E + G+P A A L+ Y P+ + L +SQSG++ D Sbjct: 299 AAGTSYHAGLVGARLFEEVAGLP-AEAYLASEFGYHMPLLSQHPFFLLLSQSGETADSRE 357 Query: 115 TVEHQRKAGAFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAA 174 + +K G V+ M N S L+ AD + L AGPE +VA+TK+Y + A L A Sbjct: 358 VLVKVKKMGYPVLTMTNTAGSTLSREADYTMLLHAGPEIAVASTKAYTAQIGVQAVLAKA 417 Query: 175 W--------AQDEALETAVADLPAQLERAFALDWSAAVTALTGA-----SGLFVLGRGYG 221 A D AL ++ A ++ +D + L G F +GRG Sbjct: 418 LGMYRQQPAANDFALRHQLSIAAAGMQTL--VDEKDQIKNLVGQYMPDQHDAFYIGRGAD 475 Query: 222 YGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAE 281 Y ++ EAALK KE +H E F+A E++HG +A++ E VLAF + D R + E Sbjct: 476 YPLSLEAALKLKEVSYVHTEGFAAGELKHGTIALISEDTPVLAFITDDATAAHTRSNLQE 535 Query: 282 FRSRGAEVL------LADPAARQAGLPAIAAHPAIEPILIVQSFYKMANALALARGCDPD 335 +RGA L LA+P LP + P + ++ + +A AL +G D D Sbjct: 536 TEARGAHTLSIVSEHLAEPTDNIV-LPDV--DPRLSALVGIIPAQLIAYYTALGKGLDVD 592 Query: 336 SPPHLNK 342 P +L K Sbjct: 593 KPRNLAK 599 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: 367 Number of extensions: 15 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: 604 Length adjustment: 33 Effective length of query: 314 Effective length of database: 571 Effective search space: 179294 Effective search space used: 179294 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