Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate GFF4361 HP15_p187g69 glucosamine--fructose-6-phosphate aminotransferase, isomerizing
Query= reanno::Caulo:CCNA_00453 (363 letters) >FitnessBrowser__Marino:GFF4361 Length = 613 Score = 133 bits (334), Expect = 1e-35 Identities = 101/315 (32%), Positives = 158/315 (50%), Gaps = 27/315 (8%) Query: 66 VVTCARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSP 125 V+ A G+S +A ARY +E A + S S + PN E L + ISQSG++ Sbjct: 299 VLILACGTSSYAGMVARYWVEAIASIPCSVEIASEYRYRQSVPN-ERQLIVVISQSGETA 357 Query: 126 DLLAAVKAAKAAG-AHAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSY---IAALV 181 D +AA++ AK+ G H +A+ NV +S + A AGPE+ VA+TK++ +A L Sbjct: 358 DTIAALEHAKSLGHRHTLAICNVPESAIVRQAALRFITRAGPEIGVASTKAFTTQLATLF 417 Query: 182 AVTQLIAAW------TEDAELTAALQDLPTALAAAWTLDWSLA--VERLKTASNLYVLGR 233 +T L+A +++ ++ LP A+ +L+ S+ +R + LGR Sbjct: 418 LLTLLLAKARGTLDASDEQRYLGEIRHLPVAVEKVLSLEPSIRKLAQRFSQKRHALFLGR 477 Query: 234 GVGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDEM 293 G + +ALE ALK KE +HAEA+ A E+ HGP+ALV D P +V A ND+ + Sbjct: 478 GRHYPIALEGALKLKEISYIHAEAYPAGELKHGPLALVDDDMPVVVVAPNDQLLEKLKAN 537 Query: 294 AAGLRARGASVLIAGGGGDAPDALPTLAS----------HPVLEPILMIQSFYRMANALS 343 +RARG + + G D T AS + L P+L + + +A ++ Sbjct: 538 MEEVRARGGELYVFADG----DTRVTSASGLHVLRMPEHYGELSPVLHVVALQLLAYHVA 593 Query: 344 VARGYDPDSPPHLNK 358 + +G D D P +L K Sbjct: 594 LVKGTDVDKPRNLAK 608 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: 387 Number of extensions: 14 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 363 Length of database: 613 Length adjustment: 33 Effective length of query: 330 Effective length of database: 580 Effective search space: 191400 Effective search space used: 191400 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