Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate 352338 BT2811 alkyl hydroperoxide reductase subunit F (NCBI ptt file)
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__Btheta:352338 Length = 523 Score = 171 bits (433), Expect = 4e-47 Identities = 112/308 (36%), Positives = 174/308 (56%), Gaps = 14/308 (4%) Query: 3 EVRHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTG 62 EV+ VI+ G GPAG SAA+Y+AR L+ + I + GGQ+ T ++N V TG Sbjct: 214 EVKEYDVIVAGGGPAGVSAAIYSARKGLR-VAIVAERVGGQVKETVGIENLIS-VPETTG 271 Query: 63 PALMERMREHAERFETEIVFDH-INAVDFAAKPYTLTGD-SATYTCDALIIATGASARYL 120 L + ++ H R+ +++ I V+ A K +T + ALIIATGAS R L Sbjct: 272 SELADNLKTHLLRYPVDLLEQRKIEKVELAGKDKLVTTSVGEKFIAPALIIATGASWRKL 331 Query: 121 GLPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRET 180 +P E ++G+GV+ C CDG FY+ K VAVVGGGN+ +E A+ LA I S VT+ + Sbjct: 332 NVPGENDYIGRGVAFCPHCDGPFYKGKQVAVVGGGNSGIEAAIDLAGICSKVTVFEFMDE 391 Query: 181 FRAEKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNNDGSFDEL-KVDGVF 239 +A+ +L ++L + + + +++ EV+G+ +T R+K+ + L ++DGVF Sbjct: 392 LKADNVLQERLKSL---PNVEVFVSSQTTEVIGNGDKLTALRIKDRKTEEERLVELDGVF 448 Query: 240 IAIGHTPNTSLFEGQL-TLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSA 298 + IG + N+S+F + T + G +V+ T+V GI+AAGDV+ Y+Q I S Sbjct: 449 VQIGLSANSSVFRDIVETNRPGEIVIDA-----HCRTNVTGIYAAGDVSTVPYKQIIISM 503 Query: 299 GAGCMAAL 306 G G AAL Sbjct: 504 GEGAKAAL 511 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: 417 Number of extensions: 24 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: 523 Length adjustment: 31 Effective length of query: 289 Effective length of database: 492 Effective search space: 142188 Effective search space used: 142188 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