Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate BPHYT_RS07410 BPHYT_RS07410 glucosamine--fructose-6-phosphate aminotransferase
Query= reanno::Caulo:CCNA_00453 (363 letters) >FitnessBrowser__BFirm:BPHYT_RS07410 Length = 605 Score = 130 bits (328), Expect = 7e-35 Identities = 99/310 (31%), Positives = 149/310 (48%), Gaps = 25/310 (8%) Query: 70 ARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSPDLLA 129 A G+S ++ A+Y +E+ A + T S D+ PN + AL + ISQSG++ D LA Sbjct: 295 ACGTSYYSGLTAKYWLESIAKIPTQVEIASEYRYRDSVPNPK-ALVVVISQSGETADTLA 353 Query: 130 AVKAAKAAG-AHAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAALVAVTQLIA 188 A+K A++ G H +++ NV S + L HAG E+ VA+TK++ LV + L A Sbjct: 354 ALKHAQSLGHKHTLSVCNVATSAMVRLTSLSFHTHAGREIGVASTKAFTTQLVGLFVLAA 413 Query: 189 AW---------TEDAELTAALQDLPTALAAAWTLD-----WSLAVERLKTASNLYVLGRG 234 ++A+ L+ LP AL A L+ WS E+ + LGRG Sbjct: 414 TLGKIRGTVSPEQEADYVRQLRHLPAALNAVLALEPQIIAWS---EKFSGKESALFLGRG 470 Query: 235 VGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDEMA 294 + +ALE ALK KE +HAEA+ A E+ HGP+ALV D P + A ND + Sbjct: 471 SHYPIALEGALKLKEISYIHAEAYPAGELKHGPLALVTDAMPVVTIAPNDALLEKLKSNL 530 Query: 295 AGLRARGASVLIAG------GGGDAPDALPTLASHPVLEPILMIQSFYRMANALSVARGY 348 ++ARG + + G + + L P+L + +A + ARG Sbjct: 531 QEVKARGGELYVFADTDTRIGSEPGIHVIRMPEHYGPLSPLLHVVPLQLLAYHTACARGT 590 Query: 349 DPDSPPHLNK 358 D D P +L K Sbjct: 591 DVDKPRNLAK 600 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: 408 Number of extensions: 13 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: 605 Length adjustment: 33 Effective length of query: 330 Effective length of database: 572 Effective search space: 188760 Effective search space used: 188760 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