Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate PP_2440 PP_2440 Alkyl hydroperoxide reductase subunit F
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__Putida:PP_2440 Length = 520 Score = 158 bits (400), Expect = 2e-43 Identities = 111/310 (35%), Positives = 165/310 (53%), Gaps = 28/310 (9%) Query: 9 VIILGSGPAGYSAAVYAARANLKPLLITGMQA---GGQLTTTTEVDNWPGDVHGLTGPAL 65 V+++G GPAG +AA+YAAR ++ TG+ A GGQ+ T ++N+ V GP L Sbjct: 214 VLVVGGGPAGAAAAIYAARKGIR----TGVAAERFGGQVLDTLAIENFIS-VQETEGPKL 268 Query: 66 MERMREHAERFETEIVFDH-----INAVDFAAKPYTLTGDSATYTCDALIIATGASARYL 120 + EH ++++ +I+ I A + L G A+ +I+ATGA R + Sbjct: 269 ATALEEHVKQYDVDIMNLQRGEALIPAAEGGLHEVRLAG-GASLKAKTVILATGARWREM 327 Query: 121 GLPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRET 180 +P E+ + G+GV+ C CDG ++ K VAV+GGGN+ VE A+ LA I + VTLI Sbjct: 328 NVPGEQEYRGRGVAYCPHCDGPLFKGKRVAVIGGGNSGVEAAIDLAGIVAQVTLIEFDSQ 387 Query: 181 FRAEKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNNDGSFD---ELKVDG 237 RA+ +L KL + I L EVLG+ VTG R K D S D E+ ++G Sbjct: 388 LRADAVLQRKLRSLPNVNVITSALTT---EVLGNGEKVTGLRYK--DRSTDEQHEVALEG 442 Query: 238 VFIAIGHTPNTSLFEGQLTLKD-GYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAIT 296 +F+ IG PNT +G + L G ++V TS+ G+FAAGDV Y+Q + Sbjct: 443 IFVQIGLLPNTDWLKGTVELSPRGEIIVDA-----KGQTSIPGVFAAGDVTTVPYKQIVI 497 Query: 297 SAGAGCMAAL 306 + G G A+L Sbjct: 498 AVGEGAKASL 507 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: 390 Number of extensions: 23 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: 520 Length adjustment: 31 Effective length of query: 289 Effective length of database: 489 Effective search space: 141321 Effective search space used: 141321 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