Align Homocysteine formation from aspartate semialdehyde (DUF39 component) (characterized)
to candidate WP_078718107.1 B5D49_RS12805 hypothetical protein
Query= reanno::Miya:8500721 (390 letters) >NCBI__GCF_900167125.1:WP_078718107.1 Length = 390 Score = 597 bits (1539), Expect = e-175 Identities = 283/385 (73%), Positives = 336/385 (87%), Gaps = 1/385 (0%) Query: 1 MASFKVNKTIAEINERIRQGKAVVLNAEEMTEAVRRMGKEKAAREIDVVTTGTFSPMCSS 60 MA+ +VNKTI EINERIR+GKAVVLNAEEMT VRR+GK KAA+E+DVVTTGTFS MCSS Sbjct: 1 MATHQVNKTIQEINERIRKGKAVVLNAEEMTAEVRRLGKVKAAKEVDVVTTGTFSTMCSS 60 Query: 61 GLLFNIGQQDPPTLKTAKVWMNDVPAYAGLAAVDSYLGATEPTEDDPLNKVYPGRFKYGG 120 G+LFNIGQ+ PP +K +++WMN VPAY+GLAAVD++LGATEP EDDPLNKV+PGRF YGG Sbjct: 61 GMLFNIGQE-PPVMKVSELWMNTVPAYSGLAAVDAFLGATEPAEDDPLNKVHPGRFVYGG 119 Query: 121 GHVIEDLVRGKAVHLRAEAYGTDCYPRKSLDKKITLSELPYAHLLNPRNCYQNYNAAVNL 180 GHVIEDLVRGKAVHL+A AYGTDCYPR+ LDK +TL++LP A L+NPRNCYQNYN AVNL Sbjct: 120 GHVIEDLVRGKAVHLKARAYGTDCYPRRKLDKDVTLADLPNAWLINPRNCYQNYNCAVNL 179 Query: 181 TSRIIYTYMGPLKPNLRNVNFATAGRISPLFNDPLFRTIGLGTRIFLGGGTGYVLGAGTQ 240 TSR IYTYMGPLKP RN NFAT+G +SPLFNDPLF+TIG+GTRIFL GG GYV+GAGTQ Sbjct: 180 TSRTIYTYMGPLKPKSRNANFATSGALSPLFNDPLFKTIGMGTRIFLAGGIGYVIGAGTQ 239 Query: 241 HVAAPKRTERGLPLSPAGTLMLKGDLKGMNARYLRGLSFLGYGCSLAVGVGIPIPILNEE 300 H P R E G+P +PAGTLM+KGD+K MNARYLRG+S +GYG SL VGVGIPIPILNEE Sbjct: 240 HNPKPPRNEYGIPTTPAGTLMVKGDMKQMNARYLRGVSVVGYGSSLNVGVGIPIPILNEE 299 Query: 301 IAWFTGVDDSDIQMPVKDYGHDYPNCLPRVIQHVTYEDLKSGEVEIMGKKVETVPMTSYP 360 IAW TGV ++DIQMPV+DYG+DYPN +PRV+ HVT E+L SGE+ + G+K+ ++P+TS+P Sbjct: 300 IAWHTGVSNADIQMPVRDYGYDYPNGVPRVLGHVTLEELMSGEIVVDGRKIPSIPVTSHP 359 Query: 361 LSLEVANTLKSWIEKGEFLLTEPVE 385 +SLEVAN LK WI G+FLL++PV+ Sbjct: 360 MSLEVANELKRWIMDGKFLLSQPVD 384 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: 593 Number of extensions: 19 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