Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate 8501344 DvMF_2077 FAD-dependent pyridine nucleotide-disulphide oxidoreductase (RefSeq)
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__Miya:8501344 Length = 602 Score = 195 bits (495), Expect = 3e-54 Identities = 128/336 (38%), Positives = 187/336 (55%), Gaps = 45/336 (13%) Query: 2 VEVRHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPG--DVHG 59 ++V + +++LG+GPAG SAA+Y R+ +K +++ GGQ+T T V+N+PG D+ G Sbjct: 265 LDVVETDMVVLGAGPAGLSAAIYGERSGMKTVVLDKSVVGGQVTVTPVVENYPGFTDIAG 324 Query: 60 LTGPALMERMREHAERFETEIVFDHINAVDFAAKPYTLTGDSATYTCDALIIATGASARY 119 L L+E + HA ++ T + ++ V K + + A Y C AL+ ATGA R Sbjct: 325 LK---LVEVLSAHARQYATVREGETVHEVKIG-KLIEVYTNRAVYLCKALVFATGAQWRK 380 Query: 120 LGLPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRE 179 L P E F G+GVS CA+CDGF YR K VA++GGGN+A+ +AL+L N+ + VT+IHRR+ Sbjct: 381 LDAPGEGRFYGRGVSYCASCDGFMYRGKRVAMIGGGNSALTDALHLKNLGADVTIIHRRD 440 Query: 180 TFRAEKILIDKLNARVAEGKIILKLNANLDEVLGDNMG---------------------- 217 +FRAEK L D L EG I + + ++E+LGD + Sbjct: 441 SFRAEKALQDSLE---REG-IAVIWDTVVEEILGDTVAPVREGDGGDGKDAAPGTAPAEP 496 Query: 218 ----VTGARLKN-NDGSFDELKVDGVFIAIGHTPNTSLFE--GQLTLKDGYLVVQGGRDG 270 V G R++N + EL DGVF+AIGH PN+ G + KDG + V Sbjct: 497 DTGVVRGIRVRNVKTDAVSELPFDGVFVAIGHIPNSEQAAELGVVLEKDGSIKVD----- 551 Query: 271 NATATSVEGIFAAGDVADHVYRQAITSAGAGCMAAL 306 T++ I+AAGDV V RQ +T+ G+G AAL Sbjct: 552 RHMRTNIPRIYAAGDVTGGV-RQIVTAVGSGATAAL 586 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: 473 Number of extensions: 28 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: 602 Length adjustment: 32 Effective length of query: 288 Effective length of database: 570 Effective search space: 164160 Effective search space used: 164160 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: 51 (24.3 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