Align Homocysteine formation from aspartate semialdehyde (DUF39 component) (characterized)
to candidate WP_027720650.1 H589_RS0102935 hypothetical protein
Query= reanno::Miya:8500721 (390 letters) >NCBI__GCF_000425265.1:WP_027720650.1 Length = 390 Score = 588 bits (1516), Expect = e-173 Identities = 275/387 (71%), Positives = 335/387 (86%), Gaps = 1/387 (0%) Query: 3 SFKVNKTIAEINERIRQGKAVVLNAEEMTEAVRRMGKEKAAREIDVVTTGTFSPMCSSGL 62 +F+VNKTI EINERI++GKAVV+NAEEM + VR GK +AA+EIDVVTTGTFSPMCSSG+ Sbjct: 4 TFEVNKTIKEINERIKKGKAVVVNAEEMVDIVRTKGKVEAAKEIDVVTTGTFSPMCSSGM 63 Query: 63 LFNIGQQDPPTLKTAKVWMNDVPAYAGLAAVDSYLGATEPTEDDPLNKVYPGRFKYGGGH 122 +FNIGQ PP +KT++VW+N+VP YAGLAAVDSYLG TEP EDDPLNKV+PGRF YGGGH Sbjct: 64 MFNIGQV-PPLMKTSQVWLNNVPCYAGLAAVDSYLGVTEPAEDDPLNKVHPGRFVYGGGH 122 Query: 123 VIEDLVRGKAVHLRAEAYGTDCYPRKSLDKKITLSELPYAHLLNPRNCYQNYNAAVNLTS 182 VIEDL+ GK V L+A+AYGTDCYPR+ ++K I+L +LP A ++NPRNCYQNYN AVN+TS Sbjct: 123 VIEDLIAGKTVRLKAKAYGTDCYPRREIEKDISLKDLPNAVMMNPRNCYQNYNCAVNMTS 182 Query: 183 RIIYTYMGPLKPNLRNVNFATAGRISPLFNDPLFRTIGLGTRIFLGGGTGYVLGAGTQHV 242 R IYTYMGPLKPN RN NFATAG++SPLFNDP +TIG+GTRIFL G GYV+GAGTQHV Sbjct: 183 RTIYTYMGPLKPNQRNANFATAGQLSPLFNDPYLKTIGMGTRIFLCGTQGYVIGAGTQHV 242 Query: 243 AAPKRTERGLPLSPAGTLMLKGDLKGMNARYLRGLSFLGYGCSLAVGVGIPIPILNEEIA 302 P+R ERG+PL+PAGTLMLKGDL+GM+ RY RG+S GYGC+ +VGVGIPIPILNEE+A Sbjct: 243 KNPQRNERGIPLTPAGTLMLKGDLEGMDPRYFRGISMTGYGCTSSVGVGIPIPILNEEMA 302 Query: 303 WFTGVDDSDIQMPVKDYGHDYPNCLPRVIQHVTYEDLKSGEVEIMGKKVETVPMTSYPLS 362 W+TGV D+DIQ+PVKDYG+DYPN + +++ HVT E+LKSG + + GK + TVPMTS+ +S Sbjct: 303 WYTGVSDADIQVPVKDYGYDYPNGVGQILAHVTMEELKSGSINLNGKDIPTVPMTSHVMS 362 Query: 363 LEVANTLKSWIEKGEFLLTEPVELLPS 389 LE+A+ LKSWIEKG+FLL+EPVE + S Sbjct: 363 LEIADKLKSWIEKGDFLLSEPVEKIES 389 Lambda K H 0.318 0.137 0.409 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: 631 Number of extensions: 20 Number of successful extensions: 2 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: 390 Length of database: 390 Length adjustment: 31 Effective length of query: 359 Effective length of database: 359 Effective search space: 128881 Effective search space used: 128881 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 Apr 10 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