Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate HSERO_RS09495 HSERO_RS09495 thioredoxin reductase
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__HerbieS:HSERO_RS09495 Length = 318 Score = 443 bits (1140), Expect = e-129 Identities = 214/313 (68%), Positives = 266/313 (84%), Gaps = 1/313 (0%) Query: 5 RHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTGPA 64 +H++V+ILGSGPAGYSAAVYAARANL P+LITG++ GGQL TTT+V+NWPGD G+ GP Sbjct: 6 KHAKVLILGSGPAGYSAAVYAARANLNPVLITGVEQGGQLMTTTDVENWPGDPLGVQGPE 65 Query: 65 LMERMREHAERFETEIVFDHINAVDFAAKPYTLTGDSATYTCDALIIATGASARYLGLPS 124 LM+R+ +HAERF+TEI+FDHI+ + +P+ L GDS YT DALIIATGASA+YLGLPS Sbjct: 66 LMQRLLQHAERFKTEIIFDHIHTTKLSERPFRLIGDSGEYTADALIIATGASAQYLGLPS 125 Query: 125 EEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETFRAE 184 E+AFMG+GVSACATCDGFFYR K VAVVGGGNTAVEEALYL+NIAS VT+IHRR+ FRAE Sbjct: 126 EQAFMGRGVSACATCDGFFYRGKEVAVVGGGNTAVEEALYLSNIASKVTIIHRRDKFRAE 185 Query: 185 KILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKN-NDGSFDELKVDGVFIAIG 243 ILID+L +V+EGKI ++ + LDEV+GD+ GVTG ++K+ D + E+ V G+FIAIG Sbjct: 186 PILIDRLLHKVSEGKIAIQWHHTLDEVVGDDSGVTGIKIKSTQDDAITEIPVHGLFIAIG 245 Query: 244 HTPNTSLFEGQLTLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAGAGCM 303 H PNTS+FEGQL++++GYL + G +G ATATS++G+FAAGDV DHVYRQAITSAG GCM Sbjct: 246 HKPNTSIFEGQLSMQNGYLKTRTGTEGFATATSIDGVFAAGDVQDHVYRQAITSAGTGCM 305 Query: 304 AALDTERYLDGLQ 316 AALD +RYL+GL+ Sbjct: 306 AALDAQRYLEGLE 318 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: 368 Number of extensions: 12 Number of successful extensions: 2 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: 318 Length adjustment: 28 Effective length of query: 292 Effective length of database: 290 Effective search space: 84680 Effective search space used: 84680 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