Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate H281DRAFT_05826 H281DRAFT_05826 glutamine--fructose-6-phosphate transaminase
Query= reanno::Caulo:CCNA_00453 (363 letters) >FitnessBrowser__Burk376:H281DRAFT_05826 Length = 605 Score = 127 bits (318), Expect = 1e-33 Identities = 97/310 (31%), Positives = 148/310 (47%), Gaps = 25/310 (8%) Query: 70 ARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSPDLLA 129 A G+S ++ A+Y +E+ A + T S ++ PN +L + ISQSG++ D LA Sbjct: 295 ACGTSYYSGLTAKYWLESIAKIPTQVEIASEYRYRESVPNPR-SLVVVISQSGETADTLA 353 Query: 130 AVKAAKAAG-AHAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAALVAVTQLIA 188 A+K A+A G H +A+ NV S + + HAG E+ VA+TK++ LVA+ L Sbjct: 354 ALKHAQALGHRHTLAVCNVGTSAMVRQTELAFLTHAGREIGVASTKAFTTQLVALFVLAV 413 Query: 189 AWT---------EDAELTAALQDLPTALAAAWTLD-----WSLAVERLKTASNLYVLGRG 234 ++ E L+ LP AL + L+ WS E + LGRG Sbjct: 414 TLAKQRGRVSPEQETEYLRQLRHLPAALNSVLALEPQIIAWS---EEFSRKEHALFLGRG 470 Query: 235 VGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDEMA 294 + + +ALE ALK KE +HAEA+ A E+ HGP+ALV + P + A ND + Sbjct: 471 MHYPIALEGALKLKEISYIHAEAYPAGELKHGPLALVTEAMPVVTVAPNDALLEKLKSNI 530 Query: 295 AGLRARGASVLIAGG------GGDAPDALPTLASHPVLEPILMIQSFYRMANALSVARGY 348 +RARG + + + + + +L PIL + +A + ARG Sbjct: 531 QEVRARGGQLYVFADADTKIVNDEGIHVIRMPEHYGLLSPILHVVPLQLLAYHTACARGT 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: 400 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: 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