Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate 3608541 Dshi_1935 cyclic nucleotide-regulated FAD-dependent pyridine nucleotide-disulphide oxidoreductase (RefSeq)
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__Dino:3608541 Length = 539 Score = 118 bits (296), Expect = 3e-31 Identities = 93/301 (30%), Positives = 140/301 (46%), Gaps = 11/301 (3%) Query: 9 VIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTGPALMER 68 V+I+G GPAG +AAVYA L L++ + GGQ T++ ++N+ G G++G L R Sbjct: 228 VLIVGGGPAGIAAAVYAGAEGLSALVVEDLTIGGQAGTSSRIENYMGFPTGISGADLCWR 287 Query: 69 MREHAERFETEIVFDH--INAVDFAAKPYTLT-GDSATYTCDALIIATGASARYLGLPSE 125 A +F T ++ AA + +T D A++IATG R L +P Sbjct: 288 GEVQAMKFGTRFAVPRRAVHVAPLAAGGFCVTLDDGEEVRTRAIVIATGVQYRKLPIPRL 347 Query: 126 EAFMGKGVSACAT-CDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETFRA- 183 E F G GV AT + + RN V V+GGGN+A + A++L+ A V ++ R + A Sbjct: 348 EEFEGAGVYYAATDVEARYCRNTDVVVIGGGNSAGQAAMFLSRSARHVHVLIRGDGLAAS 407 Query: 184 -EKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNNDGSFDELKVDGVFIAI 242 L ++L+ A I L + + G + G L+ VF+ + Sbjct: 408 MSSYLSERLDRDPA---ITLHRRTQVTGLHGTDRLEEATIRDGVMGQDWTLRTGAVFVMV 464 Query: 243 GHTPNTSLFEGQLTLKDGYLVVQGGRDGNATA--TSVEGIFAAGDVADHVYRQAITSAGA 300 G PNT +G +TL D V G G + TS GIFA GDV ++ + G Sbjct: 465 GAAPNTGWLDGLVTLDDKGFVHTGPEVGGRSTYETSCPGIFAVGDVRAGSVKRVASGVGE 524 Query: 301 G 301 G Sbjct: 525 G 525 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: 397 Number of extensions: 22 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: 539 Length adjustment: 31 Effective length of query: 289 Effective length of database: 508 Effective search space: 146812 Effective search space used: 146812 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: 50 (23.9 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