Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_057508080.1 ABB28_RS07710 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Caulo:CCNA_00453 (363 letters) >NCBI__GCF_001431535.1:WP_057508080.1 Length = 612 Score = 128 bits (322), Expect = 4e-34 Identities = 99/307 (32%), Positives = 152/307 (49%), Gaps = 19/307 (6%) Query: 70 ARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSPDLLA 129 A G+S +A ARY IE+ AG L + + Y A+ L + +SQSG++ D + Sbjct: 302 ACGTSYYAGMTARYWIESIAG-LPCNVEIASEYRYRAAYADPKHLVVTLSQSGETLDTME 360 Query: 130 AVKAAKAAG-AHAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAALVAVTQLIA 188 A+K AK+ G H +++ NV +S + ++ V AG E+ VA+TK++ L A+ QL Sbjct: 361 ALKYAKSLGHLHTLSICNVPESAIPRASELVCYTRAGAEIGVASTKAFTTQLAALFQLTV 420 Query: 189 AW---------TEDAELTAALQDLPTALAAAWTLDWSLAV--ERLKTASNLYVLGRGVGF 237 T +A+ L+ LP ++ A ++ +A ER S+ LGRG+ + Sbjct: 421 VLGKLHGRVDATREADYLEQLRFLPGSVQHALNMEPQIAAWAERFARKSSALFLGRGLHY 480 Query: 238 GVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDEMAAGL 297 +ALE ALK KE +HAEA+ A E+ HGP+ALV + P +V A ND V + Sbjct: 481 PIALEGALKLKEITYIHAEAYPAGELKHGPLALVDEDMPVVVIAPNDSLLEKVKSNMQEV 540 Query: 298 RARGASVLIAGG------GGDAPDALPTLASHPVLEPILMIQSFYRMANALSVARGYDPD 351 RARG + + + + T VL PI+ +A ++ARG D D Sbjct: 541 RARGGELFVFADQDSNFVESEGVHVIRTPRHAGVLSPIVHTIPVQLLAYHTALARGTDVD 600 Query: 352 SPPHLNK 358 P +L K Sbjct: 601 KPRNLAK 607 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: 395 Number of extensions: 17 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: 612 Length adjustment: 33 Effective length of query: 330 Effective length of database: 579 Effective search space: 191070 Effective search space used: 191070 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 24 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