Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate CCNA_02964 CCNA_02964 thioredoxin-disulfide reductase
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__Caulo:CCNA_02964 Length = 335 Score = 329 bits (843), Expect = 7e-95 Identities = 179/313 (57%), Positives = 228/313 (72%), Gaps = 12/313 (3%) Query: 5 RHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTGPA 64 R +R +I+GSGPAGY+AA+YAARA LKP+LI G+Q GGQLT TT+V+N+PG + GP Sbjct: 7 RQTRCLIIGSGPAGYTAAIYAARALLKPVLIAGIQPGGQLTITTDVENYPGFADVIQGPW 66 Query: 65 LMERMREHAERFETEIVFDHINAVDFAAKPYTLTGDSAT-YTCDALIIATGASARYLGLP 123 LM++MR AE TE V D + +VD + +P+T+ DS + + +IIATGA A++LGL Sbjct: 67 LMDQMRAQAEHVGTEFVSDIVTSVDLSKRPFTVKTDSGQDWIAETIIIATGAQAKWLGLE 126 Query: 124 SEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETFRA 183 SE F G GVSACATCDGFFYRNK V VVGGGNTAVEEAL+L + AS VTL+HR++ RA Sbjct: 127 SEAKFQGFGVSACATCDGFFYRNKDVIVVGGGNTAVEEALFLTSFASKVTLVHRKDELRA 186 Query: 184 EKILIDKLNARVAEGKIILKLNANLDEVLG--DNMGVTGARLKN-NDGSFDELKVDGVFI 240 EKIL ++L +A KI + ++ +DEVLG D MGVTGARLKN G E+ DGVFI Sbjct: 187 EKILQERL---LAHPKIEVIWDSVIDEVLGQTDPMGVTGARLKNVKTGETQEVAADGVFI 243 Query: 241 AIGHTPNTSLFEGQL-TLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAG 299 AIGH P++ LF GQL T GYL V+ G +T++EG++AAGDV D VYRQA+T+AG Sbjct: 244 AIGHAPSSELFAGQLETGSGGYLKVKPG----TASTAIEGVYAAGDVTDDVYRQAVTAAG 299 Query: 300 AGCMAALDTERYL 312 GCMAAL+ R+L Sbjct: 300 MGCMAALEAVRFL 312 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: 324 Number of extensions: 15 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: 335 Length adjustment: 28 Effective length of query: 292 Effective length of database: 307 Effective search space: 89644 Effective search space used: 89644 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