Align Homocysteine formation from aspartate semialdehyde (DUF39 component) (characterized)
to candidate WP_013705389.1 DESAC_RS01910 homocysteine biosynthesis protein
Query= reanno::Miya:8500721 (390 letters) >NCBI__GCF_000195295.1:WP_013705389.1 Length = 406 Score = 517 bits (1332), Expect = e-151 Identities = 251/389 (64%), Positives = 304/389 (78%), Gaps = 1/389 (0%) Query: 1 MASFKVNKTIAEINERIRQGKAVVLNAEEMTEAVRRMGKEKAAREIDVVTTGTFSPMCSS 60 MA+ +VNKT EINE+I++G+AVV+ AEE+ + VR+ G+ AAR +DVVTTGTFSPMCSS Sbjct: 1 MATHQVNKTYREINEKIKKGQAVVVTAEEIIDIVRQKGEVAAARTVDVVTTGTFSPMCSS 60 Query: 61 GLLFNIGQQDPPTLKTAKVWMNDVPAYAGLAAVDSYLGATEPTEDDPLNKVYPGRFKYGG 120 G+L N+G PP ++ ++ W+N VPAY+GLAAVD YLGATEPT DDPLNKVYPG FKYGG Sbjct: 61 GVLLNMGHSQPP-IRISQSWINRVPAYSGLAAVDLYLGATEPTIDDPLNKVYPGEFKYGG 119 Query: 121 GHVIEDLVRGKAVHLRAEAYGTDCYPRKSLDKKITLSELPYAHLLNPRNCYQNYNAAVNL 180 GHVI+DLV GK VHL+AE+YGTDCYPRK ++ TLSEL A LLNPRN YQNYN AVN Sbjct: 120 GHVIQDLVAGKKVHLQAESYGTDCYPRKKWERVFTLSELVNAVLLNPRNGYQNYNCAVNA 179 Query: 181 TSRIIYTYMGPLKPNLRNVNFATAGRISPLFNDPLFRTIGLGTRIFLGGGTGYVLGAGTQ 240 T +IIYTYMGPL+P L N N+ TAG++SPL NDP + TIG+GTRIFLGGG GYV GTQ Sbjct: 180 TQKIIYTYMGPLRPRLGNANYCTAGQLSPLLNDPYYLTIGIGTRIFLGGGVGYVAWPGTQ 239 Query: 241 HVAAPKRTERGLPLSPAGTLMLKGDLKGMNARYLRGLSFLGYGCSLAVGVGIPIPILNEE 300 H R + G+P+ PAGTLM+ GDLK M+ RYL G+S LGYGCSLAVG+G+PIP+LNEE Sbjct: 240 HNPQVPRAQNGVPMKPAGTLMVMGDLKQMHPRYLIGVSLLGYGCSLAVGLGVPIPLLNEE 299 Query: 301 IAWFTGVDDSDIQMPVKDYGHDYPNCLPRVIQHVTYEDLKSGEVEIMGKKVETVPMTSYP 360 IA + V D DI +PV DYG DYP+ R+I HVTY LK G +E+ G ++ T P+TS Sbjct: 300 IARYCAVTDEDILVPVVDYGEDYPHATGRIITHVTYAQLKQGVIEVEGHQINTAPLTSMV 359 Query: 361 LSLEVANTLKSWIEKGEFLLTEPVELLPS 389 S E+A TLK+WI G+FLLTEPVELLPS Sbjct: 360 RSREIAATLKNWILAGDFLLTEPVELLPS 388 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: 581 Number of extensions: 24 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: 406 Length adjustment: 31 Effective length of query: 359 Effective length of database: 375 Effective search space: 134625 Effective search space used: 134625 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 Jul 25 2024. The underlying query database was built on Jul 25 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