Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_008538534.1 HMPREF9454_RS05935 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Caulo:CCNA_00453 (363 letters) >NCBI__GCF_000245775.1:WP_008538534.1 Length = 609 Score = 120 bits (302), Expect = 7e-32 Identities = 99/315 (31%), Positives = 154/315 (48%), Gaps = 30/315 (9%) Query: 66 VVTCARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSP 125 +V C G++ HA +Y IE A + S D + E L + ISQSG++ Sbjct: 298 IVAC--GTAYHAGLVGKYYIEKLARIPVEIDIASEFRYRDPIID-EHTLTIVISQSGETS 354 Query: 126 DLLAAVKAAKAAGAHAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAALVA--- 182 D LAA+K +K GA +A+ NVV S +A AD+V+ AGPE++VA+TK+Y LV Sbjct: 355 DTLAALKESKRLGAKTLAITNVVGSSIAREADQVMYTWAGPEIAVASTKAYTTQLVTMFL 414 Query: 183 ----VTQLIAAWTEDA--ELTAALQDLPTALAAAWTLDWSLAVERLKT-------ASNLY 229 V+ L T + EL L+ LP + TL+ VE +KT ++++ Sbjct: 415 FAMYVSGLKGTITTERTHELLTQLRLLPDEINR--TLE---DVEPIKTFAKNYAFNNDVF 469 Query: 230 VLGRGVGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRAS 289 +GR + + VALE +LK KE +HAEA++A E+ HG +AL++ G P + A Sbjct: 470 YIGRSLDYNVALEGSLKLKEISYIHAEAYAAGELKHGTLALIESGVPVIALATQKSVYEK 529 Query: 290 VDEMAAGLRARGASVLIAGGGGD------APDALPTLASHPVLEPILMIQSFYRMANALS 343 ++AR A ++ D + A+ +L P+L + +A + Sbjct: 530 TLSNIKEVKARDAVMIGIAAEDDNELEKYVDHVIKVPATDELLIPLLTVVPLQLLAYYAA 589 Query: 344 VARGYDPDSPPHLNK 358 + RG D D P +L K Sbjct: 590 ITRGCDVDKPRNLAK 604 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: 347 Number of extensions: 16 Number of successful extensions: 3 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: 609 Length adjustment: 33 Effective length of query: 330 Effective length of database: 576 Effective search space: 190080 Effective search space used: 190080 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