Align 2-deoxy-3-keto-D-ribonate cleavage enzyme (characterized)
to candidate AZOBR_RS27000 AZOBR_RS27000 3-keto-5-aminohexanoate cleavage protein
Query= reanno::Burk376:H281DRAFT_00641 (312 letters) >FitnessBrowser__azobra:AZOBR_RS27000 Length = 316 Score = 427 bits (1099), Expect = e-124 Identities = 205/306 (66%), Positives = 252/306 (82%), Gaps = 2/306 (0%) Query: 6 RKVIISCAITGATHVPSMSEFLPITPEQIRDQAIEAAQAGAAIIHLHARDPVDGRPTPSP 65 +KVIISCA+TG+ H P+MS+ LP+TP++I +Q + AA+AGAAI+HLHARDP G+PTP P Sbjct: 10 KKVIISCALTGSIHTPTMSDALPVTPDEIVEQGVGAAEAGAAILHLHARDPRTGQPTPDP 69 Query: 66 EIFKAFVPAIAEATDAVINITTGGSTRMTLEERLAYPRLARPEMCSLNMGSMNFSIHPVA 125 +F F+P + ++TDAV+NITTGGS MT++ERLA P ARPEMCSLNMGSMNF I P+A Sbjct: 70 AVFMQFLPRLKQSTDAVLNITTGGSLNMTVQERLAAPLQARPEMCSLNMGSMNFGIFPLA 129 Query: 126 AKISSWRYGWEKDYIEGMEDMIFRNTFRDIRNILLELGES-GTRFEFECYDVGHLYNLAH 184 + W++ WE+ Y+ +D IFRNTFRDI IL LGE GTRFEFECYDVGHLYNLAH Sbjct: 130 DRYQGWKHDWEEPYLRSTDDFIFRNTFRDIAYILEHLGEGCGTRFEFECYDVGHLYNLAH 189 Query: 185 FVDQGLVKPPFFIQSVFGILGGLGADPENMLLMRSTADRLFGRENYHFSVLGAGRHQMPL 244 FVD+GLVKPPFF+Q++FGILGG+GA+ N++ MR TADRLFG + Y +SVL AGRHQ+P Sbjct: 190 FVDRGLVKPPFFVQTIFGILGGIGAEQRNLVFMRETADRLFGTD-YEWSVLAAGRHQIPF 248 Query: 245 VTMSAIMGGNVRVGLEDSVYLAKGVKAETNAQQVRKIRRILEELSLEIATPADARKMLGL 304 TM+A+MGGNVRVGLEDS+YL+KG A +A+QV KIRRILEELSLE+ATPA+AR ML L Sbjct: 249 TTMAAVMGGNVRVGLEDSLYLSKGRLARNSAEQVAKIRRILEELSLEVATPAEARAMLAL 308 Query: 305 KGADQV 310 KGADQV Sbjct: 309 KGADQV 314 Lambda K H 0.321 0.137 0.400 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: 337 Number of extensions: 14 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: 312 Length of database: 316 Length adjustment: 27 Effective length of query: 285 Effective length of database: 289 Effective search space: 82365 Effective search space used: 82365 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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