Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate 350082 BT0554 glucosamine--fructose-6-phosphate aminotransferase (NCBI ptt file)
Query= reanno::Caulo:CCNA_00453 (363 letters) >FitnessBrowser__Btheta:350082 Length = 614 Score = 118 bits (296), Expect = 4e-31 Identities = 94/312 (30%), Positives = 145/312 (46%), Gaps = 22/312 (7%) Query: 65 VVVTCARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKS 124 ++V C G+S HA ++LIE+ + S D + E + +AISQSG++ Sbjct: 302 IIVAC--GTSWHAGLIGKHLIESFCRIPVEVEYASEFRYRDPVID-EHDVVIAISQSGET 358 Query: 125 PDLLAAVKAAKAAGAHAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAALVAVT 184 D LAAV+ AK+ GA + N + S + +H GPE+ VA+TK++ + +T Sbjct: 359 ADTLAAVELAKSRGAFIYGICNAIGSSIPRATHTGSYIHVGPEIGVASTKAFTGQVTVLT 418 Query: 185 QLIAAW---------TEDAELTAALQDLPTALAAAWTLDWSLAVERLKT---ASNLYVLG 232 L T+ + L +P + L+ LA E KT A N LG Sbjct: 419 MLALTLAREKGTIDETQYLNIVRELNSIPGKMKEVLKLNDKLA-ELSKTFTYAHNFIYLG 477 Query: 233 RGVGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDE 292 RG + VALE ALK KE +HAE + AAE+ HGP+AL+ P +V A + V Sbjct: 478 RGYSYPVALEGALKLKEISYIHAEGYPAAEMKHGPIALIDAEMPVVVIATQNGLYEKVLS 537 Query: 293 MAAGLRARGASVLIAGGGGD------APDALPTLASHPVLEPILMIQSFYRMANALSVAR 346 ++AR V+ GD A ++ + L+P++ +A ++V + Sbjct: 538 NIQEIKARKGKVIAFVTKGDTVISKIADCSIELPETIECLDPLITTVPLQLLAYHIAVCK 597 Query: 347 GYDPDSPPHLNK 358 G D D P +L K Sbjct: 598 GMDVDQPRNLAK 609 Lambda K H 0.315 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: 329 Number of extensions: 12 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: 363 Length of database: 614 Length adjustment: 33 Effective length of query: 330 Effective length of database: 581 Effective search space: 191730 Effective search space used: 191730 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 (21.6 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