Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_072787251.1 BUA36_RS20885 SIS domain-containing protein
Query= reanno::pseudo3_N2E3:AO353_04455 (336 letters) >NCBI__GCF_900143065.1:WP_072787251.1 Length = 337 Score = 366 bits (940), Expect = e-106 Identities = 195/336 (58%), Positives = 242/336 (72%) Query: 1 MLEEALSSYKAVDAQLQQLDPLMIEIAGRLNRQPPQVAMTVARGSSDHAASYFAYLTMQH 60 ML+EALS+ V QL E+ +L A+T+ARGSSDHA +Y AYL M Sbjct: 2 MLKEALSAADCVAQQLANDGERYAELGRKLRSTSFSTALTIARGSSDHACAYVAYLIMAR 61 Query: 61 VGIPVASLPMSVVTMQQAPLKVSGQAVFAFSQSGQSPDLVNSLRLLRKRGALSISMVNAE 120 +G VASLPMS+VT+ ++PL + SQSGQSPD+V +R R GA +I++VN Sbjct: 62 LGRVVASLPMSLVTLNKSPLITRDTLAISISQSGQSPDVVEPIRYFRDGGATTIALVNDI 121 Query: 121 NSPLEAACEFSLPLCAGTESSVAATKSFIATLSASARLIAYWKQDPELLQAGLALPEGLR 180 +SPL A E+++PL AG E SVAATKSFI +L A ARL+A W+ DPELL ALPE LR Sbjct: 122 DSPLAQAAEWAMPLRAGKEQSVAATKSFITSLVAGARLVAAWQNDPELLAGLEALPESLR 181 Query: 181 DAATQDWSLAVDVLRDCQRLMVIGRGAGFAIAQEAALKLKETSAIQAEAFSSAEVKHGPM 240 A T+DWS AV+VL + +MV+GRG F +A EA+LK KETSA+QAEAFS AE+KHGPM Sbjct: 182 AATTEDWSKAVEVLTPARNIMVVGRGISFPVALEASLKFKETSALQAEAFSGAEIKHGPM 241 Query: 241 ALIDDNYPLLVFAPRGAEQAGLLSLAAEMRQRGARVLLAAPDDVSERDLTLSRAEHPALD 300 ALI++ YPL++FA RG QA LL LA EMR RGARVLLAAP DV++RDLTL A P LD Sbjct: 242 ALIEEGYPLVIFATRGPTQASLLQLATEMRGRGARVLLAAPADVADRDLTLPVAATPDLD 301 Query: 301 PILAIQSFYVMAAGLAVARGMDPDQPRHLSKVTRTH 336 PI+A+Q+FY MAA L+ ARG+DPDQPRHLSKVT+T+ Sbjct: 302 PIVAVQAFYKMAAELSAARGLDPDQPRHLSKVTKTN 337 Lambda K H 0.318 0.130 0.362 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: 337 Number of extensions: 7 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: 336 Length of database: 337 Length adjustment: 28 Effective length of query: 308 Effective length of database: 309 Effective search space: 95172 Effective search space used: 95172 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 (21.8 bits) S2: 49 (23.5 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