Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate SMc01224 SMc01224 thioredoxin reductase
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__Smeli:SMc01224 Length = 324 Score = 314 bits (804), Expect = 2e-90 Identities = 169/319 (52%), Positives = 223/319 (69%), Gaps = 16/319 (5%) Query: 5 RHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTGPA 64 RH++V+I+GSGPAGY+AA+Y ARA L P+LI GM+ GGQL TT+V+N+PG + GP Sbjct: 4 RHTKVLIIGSGPAGYTAAIYTARAMLSPVLIAGMEQGGQLMITTDVENYPGYADPVQGPW 63 Query: 65 LMERMREHAERFETEIVFDHINAVDFAAKPYTLTGDSAT-YTCDALIIATGASARYLGLP 123 +ME+M A TEIV D + VD + +P+ + DS T +T DALIIATGA A++LG+ Sbjct: 64 MMEQMLNQAIHVGTEIVNDLVTDVDLSVRPFRIKTDSGTDWTADALIIATGAKAKWLGIE 123 Query: 124 SEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETFRA 183 +E FMG GVSACATCDGFFYRNK V VVGGGN+AVEEALYL+N+A TVT++HRR+ FRA Sbjct: 124 TEPTFMGFGVSACATCDGFFYRNKEVIVVGGGNSAVEEALYLSNLAKTVTVVHRRDAFRA 183 Query: 184 EKILIDKLNARVAEGKIILKLNANLDEVLGD------NMGVTGARLKN-NDGSFDELKVD 236 EKIL ++L A+ + + + + E LG V G +L+N G ++ +D Sbjct: 184 EKILQERL---FAKPNVKVIWDHEVLEYLGTPAKPPMPASVNGVKLRNTKTGETSDMAID 240 Query: 237 GVFIAIGHTPNTSLFEGQLTLK-DGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAI 295 GVF+AIGH P LF+G+L K +GYL ++TAT V G+FAAGDV D +YRQA+ Sbjct: 241 GVFVAIGHAPAVELFKGKLRQKPNGYLWTA----PDSTATDVAGVFAAGDVTDDIYRQAV 296 Query: 296 TSAGAGCMAALDTERYLDG 314 T+AG GCMAAL+ E+YL G Sbjct: 297 TAAGMGCMAALEAEKYLAG 315 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: 303 Number of extensions: 17 Number of successful extensions: 4 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: 324 Length adjustment: 28 Effective length of query: 292 Effective length of database: 296 Effective search space: 86432 Effective search space used: 86432 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