Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_086509029.1 BZY95_RS05805 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Caulo:CCNA_00453 (363 letters) >NCBI__GCF_002151265.1:WP_086509029.1 Length = 611 Score = 136 bits (343), Expect = 1e-36 Identities = 114/340 (33%), Positives = 166/340 (48%), Gaps = 33/340 (9%) Query: 41 AVQLTANAPKIQALAQRLRANPPRVVVTCARGSSDHAATFARYLIETKAGVLTSSAGPSV 100 AV + P +AL +R++ +V C G+S HA ARY +E A + V Sbjct: 278 AVPVECFGPDAEALFERVKQVH---IVAC--GTSYHAGLVARYWLERYADIPVQV---EV 329 Query: 101 SSVYDASPNL--EGALYLAISQSGKSPDLLAAVKAAKAAG-AHAVALVNVVDSPLAALAD 157 +S Y + + L++ +SQSG++ D LAA++ A+ G ++A+ NV S L +D Sbjct: 330 ASEYRYRTVVVPDDTLFVTLSQSGETADTLAALRFARERGYLGSLAICNVPGSSLVRESD 389 Query: 158 EVIPLHAGPELSVAATKSYIAALVAVTQL---------IAAWTEDAELTAALQDLPTALA 208 + AGPE+ VA+TK++ L A+ L +AA T+ AEL A L+ LP + Sbjct: 390 LTLMTQAGPEIGVASTKAFTTQLTALMLLTLALGRVKGLAAETQ-AELVAGLRSLPQLVG 448 Query: 209 AAWTLDWSLAVERLKTA----SNLYVLGRGVGFGVALEAALKFKETCGLHAEAFSAAEVL 264 LD A+ERL TA + LGRG F +ALE ALK KE +HAEA+ A E+ Sbjct: 449 QVLKLDD--AIERLSTAFAEKHHALFLGRGAHFPIALEGALKLKEISYIHAEAYPAGELK 506 Query: 265 HGPMALVKDGFPALVFAQNDESRASVDEMAAGLRARGASVLIAGG------GGDAPDALP 318 HGP+ALV P + A NDE + +RARG + + D L Sbjct: 507 HGPLALVDSEMPVISVAPNDELLDKLKSNLQEVRARGGELFVFADEQVGIVEEDGVRVLH 566 Query: 319 TLASHPVLEPILMIQSFYRMANALSVARGYDPDSPPHLNK 358 H L PIL ++ ++V +G D D P +L K Sbjct: 567 LPHVHDALAPILYTVPLQLLSYHVAVLKGTDVDQPRNLAK 606 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: 435 Number of extensions: 22 Number of successful extensions: 5 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: 611 Length adjustment: 33 Effective length of query: 330 Effective length of database: 578 Effective search space: 190740 Effective search space used: 190740 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