Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate GFF2446 PGA1_c24780 thioredoxin reductase TrxB
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__Phaeo:GFF2446 Length = 313 Score = 325 bits (832), Expect = 1e-93 Identities = 177/317 (55%), Positives = 223/317 (70%), Gaps = 13/317 (4%) Query: 1 MVEVRHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGL 60 M + RH++V+I+GSGPAGY+A VYA+RA L+P+L+ G++ GGQLTTTTEV+NWPGD + Sbjct: 1 MSDTRHTKVLIIGSGPAGYTAGVYASRAMLEPILVQGIEPGGQLTTTTEVENWPGDTE-V 59 Query: 61 TGPALMERMREHAERFETEIVFDHINAVDFAAKPYTLTGDSAT-YTCDALIIATGASARY 119 GP LM RM++HA+ EI+ D I +D ++P+ GDS T YT DA+I+ATGA A++ Sbjct: 60 QGPDLMVRMQDHAKAMGCEIIGDIITDLDTTSRPFVAKGDSGTIYTADAVILATGARAKW 119 Query: 120 LGLPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRE 179 LGLPSEE F G GVSACATCDGFFYR + + V+GGGNTAVEEAL+L N AS VTLIHRR+ Sbjct: 120 LGLPSEEKFKGFGVSACATCDGFFYRGQEIVVIGGGNTAVEEALFLTNFASKVTLIHRRD 179 Query: 180 TFRAEKILIDKLNARVAEGKIILKLNANLDEVLG--DNMGVTGARLKN-NDGSFDELKVD 236 RAEKIL D+L + KI L+EV+G + +GV R+KN E+ Sbjct: 180 ELRAEKILQDRL---MKNPKIEPLWFHQLEEVVGTENPLGVEAVRVKNVKTDEITEIPCK 236 Query: 237 GVFIAIGHTPNTSLFEGQL-TLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAI 295 GVF+AIGH P T L + L T GY+ V G T TS+ GIFAAGD+ DH YRQA+ Sbjct: 237 GVFVAIGHAPATELVKDVLETHNGGYVKVTPG----TTETSIPGIFAAGDLTDHKYRQAV 292 Query: 296 TSAGAGCMAALDTERYL 312 TSAG GCMAALD ER+L Sbjct: 293 TSAGMGCMAALDAERFL 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: 317 Number of extensions: 17 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: 313 Length adjustment: 27 Effective length of query: 293 Effective length of database: 286 Effective search space: 83798 Effective search space used: 83798 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