Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate AZOBR_RS26680 AZOBR_RS26680 ABC transporter permease
Query= BRENDA::A5F699 (292 letters) >FitnessBrowser__azobra:AZOBR_RS26680 Length = 306 Score = 141 bits (356), Expect = 2e-38 Identities = 95/284 (33%), Positives = 140/284 (49%), Gaps = 7/284 (2%) Query: 4 GSIVALITPFTPDGEVDYISLKKLVDFHVDAGTDAIVSVGTTGESATLTVEEHVKVVAKT 63 G + A TP T DG +D + K L + G D +V +G TGE L E + A T Sbjct: 9 GILPATPTPVTADGTIDVAASKALFSWLNRQGIDGVVPLGGTGEYGALARAERNRFAALT 68 Query: 64 VEFAEGRLPIIAGTGANATHEAVTFSRLLNNTGIAGYLSVTPYYNKPTQEGLFLHYNAIA 123 VE +G+ P+IAG H+A+ R G+ G L +TPYY PTQ G+ ++ A Sbjct: 69 VEAMDGKKPVIAGVLDTGYHDALAAGRDFAAAGVDGLLVLTPYYTNPTQAGIRDYFLRYA 128 Query: 124 QETDIPVILYNVPGRTAVDMRPETVARLSEIKNIVALKDATGDLSRVAKHREMCKEGFVL 183 E+ +P+++Y +P RT + + PE + LS + IV +K D+ + F + Sbjct: 129 DESPVPILIYEIPYRTRIAVDPEVLHELSRHERIVGMKACNTDMYHFLRTMAGLDPSFAM 188 Query: 184 LSGDDATGLEFVKLGGQGVISVTNNIAAADMAKMMHLALDGKFDEAASINQRLMTLHKNL 243 LSG+D V G +G I VT N+ + LA GK EA +++ L+ + Sbjct: 189 LSGEDTLFPLHVAAGAKGGIVVTANLLPRAWRLVFDLASSGKTAEALEVHRTLIPMMNLA 248 Query: 244 FIESSPIPVKWAAHKMGLI-ANGDLRLPLTQLSEPARPIVAQAL 286 F E++P P+K MGLI N LP L EP RP + +AL Sbjct: 249 FAETNPGPMK---SVMGLIGVNAPAMLP--PLREP-RPELREAL 286 Lambda K H 0.318 0.134 0.379 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: 199 Number of extensions: 9 Number of successful extensions: 1 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: 292 Length of database: 306 Length adjustment: 27 Effective length of query: 265 Effective length of database: 279 Effective search space: 73935 Effective search space used: 73935 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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