Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate WP_011383106.1 AMB_RS03410 thioredoxin-disulfide reductase
Query= curated2:Q93HX6 (320 letters) >NCBI__GCF_000009985.1:WP_011383106.1 Length = 316 Score = 347 bits (889), Expect = e-100 Identities = 183/312 (58%), Positives = 234/312 (75%), Gaps = 12/312 (3%) Query: 6 HSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTGPAL 65 HS+V+ILGSGPAG +AA+YAARANL+P+L+ G+Q GGQLT TT+V+N+PG + GP L Sbjct: 5 HSKVLILGSGPAGCTAAIYAARANLEPMLVAGLQPGGQLTITTDVENFPGFAEAVQGPWL 64 Query: 66 MERMREHAERFETEIVFDHINAVDFAAKPYTLTGDSA-TYTCDALIIATGASARYLGLPS 124 ME+M+ AE T + D I +VD + +P+T GDS TY D LII TGA+AR+LGL S Sbjct: 65 MEQMQAQAEHVGTRFMDDTIVSVDLSKRPFTAVGDSGDTYAGDTLIICTGATARWLGLES 124 Query: 125 EEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETFRAE 184 E+ F G GVSACATCDGFF+R K VAV+GGGN+AVEEA+YLA IAS VTLIHRR+T RAE Sbjct: 125 EKKFSGFGVSACATCDGFFFRGKEVAVMGGGNSAVEEAIYLAGIASKVTLIHRRDTLRAE 184 Query: 185 KILIDKLNARVAEGKIILKLNANLDEVLGDN--MGVTGARLKN-NDGSFDELKVDGVFIA 241 KI D+L A K+ + ++ +DE++GD+ GVTG RLKN G+ L VDGVFIA Sbjct: 185 KIAQDRL---FANPKVAVVWDSVIDEIVGDDNPPGVTGVRLKNVKTGALSVLPVDGVFIA 241 Query: 242 IGHTPNTSLFEGQLTL-KDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAGA 300 IGHTPNT LF+G L + +GYL+ + G AT+T++ G+FAAGDV D +YRQA+T+AG Sbjct: 242 IGHTPNTELFKGALEMDSEGYLITKAG----ATSTNIPGVFAAGDVQDKIYRQAVTAAGT 297 Query: 301 GCMAALDTERYL 312 GCMAAL+ ER+L Sbjct: 298 GCMAALEAERFL 309 Lambda K H 0.318 0.135 0.386 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: 326 Number of extensions: 12 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: 320 Length of database: 316 Length adjustment: 27 Effective length of query: 293 Effective length of database: 289 Effective search space: 84677 Effective search space used: 84677 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 (21.7 bits) S2: 48 (23.1 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