Align Homocysteine formation from aspartate semialdehyde (DUF39 component) (characterized)
to candidate WP_028584881.1 G494_RS0112915 hypothetical protein
Query= reanno::Miya:8500721 (390 letters) >NCBI__GCF_000429965.1:WP_028584881.1 Length = 397 Score = 400 bits (1028), Expect = e-116 Identities = 199/383 (51%), Positives = 263/383 (68%), Gaps = 1/383 (0%) Query: 6 VNKTIAEINERIRQGKAVVLNAEEMTEAVRRMGKEKAAREIDVVTTGTFSPMCSSGLLFN 65 + KT AEINE+I GKAVVL AEE+ + V R G +KAA+E+DVVTT TF PMCSSG N Sbjct: 1 MTKTYAEINEKIAAGKAVVLTAEEVIDYVDRHGLDKAAQEVDVVTTATFGPMCSSGCFLN 60 Query: 66 IGQQDPPTLKTAKVWMNDVPAYAGLAAVDSYLGATEPTEDDPLNKVYPGRFKYGGGHVIE 125 G P ++ ++ W+ DVPAY G+AAVD YLGATE ++DP N +PG F+YGGGHVIE Sbjct: 61 FGHSTPK-MRISEAWIADVPAYCGIAAVDVYLGATELRQNDPANMYFPGEFRYGGGHVIE 119 Query: 126 DLVRGKAVHLRAEAYGTDCYPRKSLDKKITLSELPYAHLLNPRNCYQNYNAAVNLTSRII 185 DLV GK + L +YGTD YPR+ + +++L A + NPRNCYQNYN AVN + + I Sbjct: 120 DLVAGKKLQLFGLSYGTDDYPRREIRTMFDINDLNQAIMTNPRNCYQNYNVAVNCSDKTI 179 Query: 186 YTYMGPLKPNLRNVNFATAGRISPLFNDPLFRTIGLGTRIFLGGGTGYVLGAGTQHVAAP 245 +TY+G LKP +RN+ + +AG+++PL NDP ++TIG+GT ++L G G V GTQH + Sbjct: 180 HTYLGILKPRMRNMTYCSAGQLAPLLNDPTYQTIGVGTSVWLAGARGIVYAQGTQHCSEV 239 Query: 246 KRTERGLPLSPAGTLMLKGDLKGMNARYLRGLSFLGYGCSLAVGVGIPIPILNEEIAWFT 305 +R +P+ AGTL L GD+K M ++RG SF GYGC+LA+GVGIPIPILN EI T Sbjct: 240 ERGANEVPVEGAGTLGLSGDMKQMLPEFVRGASFKGYGCTLALGVGIPIPILNPEILKRT 299 Query: 306 GVDDSDIQMPVKDYGHDYPNCLPRVIQHVTYEDLKSGEVEIMGKKVETVPMTSYPLSLEV 365 V D DI V DY DYP +V+ YE L+SG+VE+ G+KV ++SY +L++ Sbjct: 300 TVRDRDISACVIDYASDYPQKTGKVLARFNYEQLRSGQVELDGRKVAVSSISSYHKALKI 359 Query: 366 ANTLKSWIEKGEFLLTEPVELLP 388 N LK+ IE G FLL+EP + LP Sbjct: 360 CNLLKAEIEDGSFLLSEPSQRLP 382 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: 503 Number of extensions: 13 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: 397 Length adjustment: 31 Effective length of query: 359 Effective length of database: 366 Effective search space: 131394 Effective search space used: 131394 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