Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate HSERO_RS22765 HSERO_RS22765 iron dicitrate transport regulator FecR
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4831 (340 letters) >FitnessBrowser__HerbieS:HSERO_RS22765 Length = 337 Score = 379 bits (973), Expect = e-110 Identities = 203/336 (60%), Positives = 250/336 (74%) Query: 5 MLEEALSSFEAVQAQLQQLDPQMIEIAGRLRRQPPQVAMTVARGSSDHAASYFAYLTMQL 64 ML+EA S+ + V QL + + + RLR PP +TVARGSSDHAA+Y AYL M Sbjct: 2 MLKEARSAADYVAVQLTRDQDRYAALGARLRAAPPANIVTVARGSSDHAATYCAYLIMAR 61 Query: 65 LGIPVASLPMSVVTMQQAPLKVSGQVAFAFSQSGQSPDLVNSLRLLRKRGALSISLVNAE 124 LG VASLPMS+VT+ APL+V +A A SQSGQSPD+V +R +GA +++LVN Sbjct: 62 LGRIVASLPMSLVTLNHAPLQVRDALAIAVSQSGQSPDVVEPIRYFHAQGATTVALVNQA 121 Query: 125 DSPLEAACEFSLPLCAGTESSVAATKSFIATLSASARLIGHWKEDTELLDACRALPEGLR 184 DSPL +A ++SLPL AG ESSVAATKSFIA+L ASA L HW++D LL+A LP+ LR Sbjct: 122 DSPLASAAQWSLPLHAGVESSVAATKSFIASLVASALLTAHWQDDAALLNALAQLPDALR 181 Query: 185 DAAQQDWSQAIDALRDCQRLMVIGRGAGFAIAQEAALKFKETSAIQAEAFSSAEVRHGPM 244 A DWS A+ AL R+MV+GRG GF +A EAALK KET AIQAEAFS AE++HGP+ Sbjct: 182 AACACDWSDAVQALTPADRIMVVGRGIGFPLALEAALKCKETCAIQAEAFSGAEIKHGPI 241 Query: 245 ALIGDNYPLLVFAPRGAEQAGLLSLAADMRQRGALVLLAAPDDVLERDLTLTRAEHPALD 304 ALI + YPLL+FA RG QAG+L+LAA+MR RGA VLLAAP+DV+ERDLTL A P LD Sbjct: 242 ALIEEGYPLLMFAIRGPSQAGMLALAAEMRVRGAKVLLAAPEDVVERDLTLPVAATPDLD 301 Query: 305 PILAIQSFYVMAAGLAVARGMDPDQPRHLSKVTRTH 340 PI+AIQ+FYVMAA L+ ARGMD D+PRHL+KVT+T+ Sbjct: 302 PIVAIQAFYVMAAQLSAARGMDADRPRHLNKVTKTN 337 Lambda K H 0.319 0.131 0.366 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: 336 Number of extensions: 9 Number of successful extensions: 1 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: 340 Length of database: 337 Length adjustment: 28 Effective length of query: 312 Effective length of database: 309 Effective search space: 96408 Effective search space used: 96408 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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