Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate N515DRAFT_0590 N515DRAFT_0590 glutamine--fructose-6-phosphate transaminase
Query= reanno::Caulo:CCNA_00453 (363 letters) >FitnessBrowser__Dyella79:N515DRAFT_0590 Length = 344 Score = 396 bits (1017), Expect = e-115 Identities = 208/340 (61%), Positives = 249/340 (73%), Gaps = 1/340 (0%) Query: 25 ASTHMFREAGEAARVAAVQLTANAPKIQALAQRLRANPPRVVVTCARGSSDHAATFARYL 84 + T M+REA E+A V QL ANA ++AL +RLRA PPR +VTCARGSSDHAA +A+Y+ Sbjct: 5 SDTLMYREAHESADVVERQLAANADVLKALGERLRAEPPRFIVTCARGSSDHAAAYAKYV 64 Query: 85 IETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSPDLLAAVKAAKAAGAHAVAL 144 ET+ G+LT+SA PSV+S+YDA L+GAL+L ISQSGKSPDLL + +AAK AGA VA+ Sbjct: 65 FETRLGLLTASASPSVASIYDADLKLDGALFLVISQSGKSPDLLRSAQAAKDAGALVVAM 124 Query: 145 VNVVDSPLAALADEVIPLHAGPELSVAATKSYIAALVAVTQLIAAWTEDAELTAALQDLP 204 VNV DSPLAALAD VIPL AGPELSVAATKSY+A L A+ QL A W D L A + LP Sbjct: 125 VNVEDSPLAALADTVIPLRAGPELSVAATKSYLATLAAILQLTAHWGNDDTLHADVARLP 184 Query: 205 TALAAAWTLDWSLAVERLKTASNLYVLGRGVGFGVALEAALKFKETCGLHAEAFSAAEVL 264 L W DWS V+ L+ A NL+V+GRG GFG ALEAALK KETCGLHAEAFSAAEV Sbjct: 185 ADLRRGWDADWSALVDGLREARNLFVVGRGYGFGAALEAALKLKETCGLHAEAFSAAEVK 244 Query: 265 HGPMALVKDGFPALVFAQNDESRASVDEMAAGLRARGASVLIAGGGGDAPDALPTLAS-H 323 HGPMA+V GFP L FAQ D++ S +A RARGA VL+A G DALP A Sbjct: 245 HGPMAIVGAGFPVLFFAQGDDTLDSTLAVAEEFRARGARVLVAKPGASGADALPLPAGMD 304 Query: 324 PVLEPILMIQSFYRMANALSVARGYDPDSPPHLNKVTETI 363 ++ P+L +QSFYR + L++ARG+DPD PPHL KVTET+ Sbjct: 305 SIVTPLLAVQSFYRATSELALARGFDPDVPPHLRKVTETV 344 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: 375 Number of extensions: 10 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: 344 Length adjustment: 29 Effective length of query: 334 Effective length of database: 315 Effective search space: 105210 Effective search space used: 105210 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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