Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate CCNA_00117 CCNA_00117 glucosamine-fructose-6-phosphate aminotransferase, isomerizing
Query= reanno::Caulo:CCNA_00453 (363 letters) >FitnessBrowser__Caulo:CCNA_00117 Length = 606 Score = 128 bits (321), Expect = 5e-34 Identities = 104/313 (33%), Positives = 154/313 (49%), Gaps = 25/313 (7%) Query: 66 VVTCARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLE-GALYLAISQSGKS 124 +V C G+S A +YLIE A + S +P L G+L +A+SQSG++ Sbjct: 294 IVAC--GTSYIAGVIGKYLIEQLADLPVDVE--IASEFRYRTPALRPGSLVVAMSQSGET 349 Query: 125 PDLLAAVKAAKAAGAHAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAAL-VAV 183 D LAA++ KA G + +VN +S +A D V P+H GPE+ VA+TK++ A + V + Sbjct: 350 ADTLAALRYCKAKGMKSAVVVNAQESTMAREVDVVWPIHCGPEIGVASTKAFTAQVSVMI 409 Query: 184 TQLIAA--------WTEDAELTAALQDLPTALAAAWTLD---WSLAVERLKTASNLYVLG 232 IAA E+ L L + P +A A L+ +A + K LY LG Sbjct: 410 ALAIAAAKARGTIDAAEEQRLVKVLLEAPRLIAEAIGLEDAIKEIAADVAKARDVLY-LG 468 Query: 233 RGVGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDE 292 RG +ALE ALK KE +HAE ++A E+ HGP+ALV D P ++ A D Sbjct: 469 RGPMSALALEGALKLKEISYIHAEGYAAGELKHGPIALVDDQTPIVILAPYDSYFEKSAS 528 Query: 293 MAAGLRARGASVLI---AGGGGDAPDALPTL----ASHPVLEPILMIQSFYRMANALSVA 345 + + ARG V+ G AP + AS P++ ++M +A ++V Sbjct: 529 NMSEVMARGGQVIFITDTEGVKHAPAGAKVVVTAPASDPLVSTLVMSAPIQLLAYHVAVV 588 Query: 346 RGYDPDSPPHLNK 358 +G D D P +L K Sbjct: 589 KGADVDQPRNLAK 601 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: 416 Number of extensions: 20 Number of successful extensions: 2 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: 606 Length adjustment: 33 Effective length of query: 330 Effective length of database: 573 Effective search space: 189090 Effective search space used: 189090 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