Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_092350588.1 BLU87_RS15755 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Phaeo:GFF2746 (342 letters) >NCBI__GCF_900107645.1:WP_092350588.1 Length = 609 Score = 129 bits (323), Expect = 3e-34 Identities = 104/357 (29%), Positives = 172/357 (48%), Gaps = 30/357 (8%) Query: 7 MRREIDEIPTAVDRLLSHGRVEIE---------AVADAARALDPNVMVTVARGSSDHVCT 57 M +EI E P A+ ++ GR++ E ++DA A + + +A G+S H Sbjct: 252 MLKEIYEQPRALADTIA-GRLQSEEGNIYLEDFGLSDAQLAGLDKIFI-IACGTSWHAGL 309 Query: 58 YLKYASEIMLGVPVASVGPSVASIYKAPLRLKGALSLAVSQSGKSPDIVSMAGSARKDGA 117 K+ E + +PV + + Y+ P+ +L++ +SQSG++ D ++ A+ G Sbjct: 310 VGKFYIEKLARIPV-EIDIASEFRYRDPIVTDKSLTILISQSGETADTLAALREAKGKGG 368 Query: 118 LSVALTNDAASPLAAAADHTLDIHAGPELSVAATKTFVTSAVAGLWLLAQWDRNQAVLAA 177 SV + N S +A +D + HAGPE+ VA+TK F T VA L + R+ L A Sbjct: 369 KSVCICNVVDSSIARESDGVIYTHAGPEIGVASTKAFTTQLVALYLLALKLGRSCGTLTA 428 Query: 178 ---------LHALPEQLDRACRID---WPEVRDAIGARSSLFTLGRGQALAVSNEAALKF 225 L ALP +L+ +D RD++ AR L+ LGRG ++ E ALK Sbjct: 429 DSCRDKVEDLLALPRKLEETLELDEQIEKIARDSMNARDFLY-LGRGNQYPIALEGALKL 487 Query: 226 KETCQLHAESYSSAEVLHGPVSIVEEGFPVLGFAAADAAEGALAGIADQIAAKGAQVFAT 285 KE +HAE Y + E+ HGP+++++E PV+ + + +++ A+G +V A Sbjct: 488 KEISYIHAEGYPAGEMKHGPIALIDENLPVVVLVPQNNIYDKVVSNMEEVCARGGKVIAI 547 Query: 286 T--DKVTAARRVDHVRTDHALTD---PISLIVSFYAMVEAFAASRGIDPDAPRHLKK 337 T ++ +VD + TD PI + + A +G D D PR+L K Sbjct: 548 TSGEESGLQGKVDTLIQVPQTTDDLMPILTSIPMQLLAYHIAVLKGTDVDQPRNLAK 604 Lambda K H 0.317 0.129 0.364 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: 10 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: 342 Length of database: 609 Length adjustment: 33 Effective length of query: 309 Effective length of database: 576 Effective search space: 177984 Effective search space used: 177984 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