Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate WP_054656330.1 CES79_RS02780 alkyl hydroperoxide reductase subunit F
Query= curated2:Q93HX6 (320 letters) >NCBI__GCF_002217945.1:WP_054656330.1 Length = 517 Score = 143 bits (361), Expect = 8e-39 Identities = 108/302 (35%), Positives = 150/302 (49%), Gaps = 16/302 (5%) Query: 9 VIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTGPALMER 68 V+I+G GPA SAAVYA R L ++ GGQ T ++N G + + G LM+ Sbjct: 214 VLIIGGGPAAGSAAVYAGRKGLSTAVVAD-HMGGQPLETVGIENLIGTDY-IEGEQLMQN 271 Query: 69 MREHAERFETEIVFDHINAVDFAAKPY--TLTGDSATYTCDALIIATGASARYLGLPSEE 126 ++ ++ ++ A P +L GD+ +IIATGA R + +P E Sbjct: 272 IQAQMTKYNVTLIDGQTVTGLTAGSPVQVSLKGDTILKG-RTVIIATGAHWRNVNVPGEA 330 Query: 127 AFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETFRAEKI 186 F KGV+ C CDG Y+ K VAV+GGGN+ VE A+ LA IA V+++ A+ + Sbjct: 331 EFRNKGVAYCPHCDGPLYKGKNVAVIGGGNSGVEAAIDLAGIAKHVSVLEFVPKISADAV 390 Query: 187 LIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNN-DGSFDELKVDGVFIAIGHT 245 L+ K + + L NA + GD VTG + G L VDGVF+ IG Sbjct: 391 LVSKAQSL---ANVDLITNAQTTAITGDGR-VTGMTYTDRATGDSKSLAVDGVFVQIGLV 446 Query: 246 PNTS-LFEGQLTLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAGAGCMA 304 PNT L E K G +VV ATS+ +FAAGD + Y+Q I S G+G A Sbjct: 447 PNTDWLAECVDMNKHGEIVVD-----EKGATSMANVFAAGDCTNSTYKQIIISMGSGATA 501 Query: 305 AL 306 AL Sbjct: 502 AL 503 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: 23 Number of successful extensions: 3 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: 517 Length adjustment: 31 Effective length of query: 289 Effective length of database: 486 Effective search space: 140454 Effective search space used: 140454 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 24 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