Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate GFF1988 Psest_2031 thioredoxin-disulfide reductase
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__psRCH2:GFF1988 Length = 315 Score = 463 bits (1191), Expect = e-135 Identities = 230/314 (73%), Positives = 264/314 (84%), Gaps = 1/314 (0%) Query: 1 MVEVRHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGL 60 M EV+HSR+IILGSGPAGY+AAVYAARANLKPL+ITG+Q GGQLTTTTEVDNWPGDV GL Sbjct: 1 MSEVKHSRLIILGSGPAGYTAAVYAARANLKPLMITGIQPGGQLTTTTEVDNWPGDVEGL 60 Query: 61 TGPALMERMREHAERFETEIVFDHINAVDFAAKPYTLTGDSATYTCDALIIATGASARYL 120 TGP LM RM++HAERF+TEIVFDHI+ + +P+TL GDSA YTCDALIIATGASA+YL Sbjct: 61 TGPDLMVRMQKHAERFDTEIVFDHIHTAELQQRPFTLRGDSAVYTCDALIIATGASAQYL 120 Query: 121 GLPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRET 180 GLPSEEAF G+GVSACATCDGFFYRN+ VAV+GGGNTAVEEALYL+NIA V LIHRR+ Sbjct: 121 GLPSEEAFAGRGVSACATCDGFFYRNQVVAVIGGGNTAVEEALYLSNIAKEVHLIHRRDK 180 Query: 181 FRAEKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNN-DGSFDELKVDGVF 239 R+EKIL DK+ + G I L N L+EVLGD GVTG RLK+ G + L + GVF Sbjct: 181 LRSEKILQDKIMDKATNGNIRLHWNHTLEEVLGDASGVTGVRLKSTLTGEENRLDLAGVF 240 Query: 240 IAIGHTPNTSLFEGQLTLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAG 299 IAIGH PNT LF+GQL +KDGYL ++GG +G+AT TS+ G+FAAGDVADHVYRQAITSAG Sbjct: 241 IAIGHKPNTDLFQGQLDMKDGYLKIRGGGEGDATCTSIPGVFAAGDVADHVYRQAITSAG 300 Query: 300 AGCMAALDTERYLD 313 AGCMAALD E+YLD Sbjct: 301 AGCMAALDAEKYLD 314 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: 405 Number of extensions: 10 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: 315 Length adjustment: 27 Effective length of query: 293 Effective length of database: 288 Effective search space: 84384 Effective search space used: 84384 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