Align Homocysteine formation from aspartate semialdehyde (DUF39 component) (characterized)
to candidate WP_092481846.1 BM299_RS02330 hypothetical protein
Query= reanno::Miya:8500721 (390 letters) >NCBI__GCF_900115975.1:WP_092481846.1 Length = 398 Score = 444 bits (1143), Expect = e-129 Identities = 217/386 (56%), Positives = 278/386 (72%), Gaps = 2/386 (0%) Query: 6 VNKTIAEINERIRQGKAVVLNAEEMTEAVRRMGKEKAAREIDVVTTGTFSPMCSSGLLFN 65 V KT EINERI+ GKAVV+ AEE+ V+ G + A E+DVVTTGTF PMCSSG N Sbjct: 3 VEKTFQEINERIKAGKAVVVTAEELVSMVKEKGVTRVASEVDVVTTGTFGPMCSSGAFLN 62 Query: 66 IGQQDPPTLKTAKVWMNDVPAYAGLAAVDSYLGATEPTEDDPLNKVYPGRFKYGGGHVIE 125 G P +K KVW+N+V AY G+AAVD+Y+GATE EDDPLN +PG+F+YGGGHVI+ Sbjct: 63 FGHSRP-RIKMHKVWLNNVAAYTGIAAVDAYIGATEVPEDDPLNSQHPGKFRYGGGHVIQ 121 Query: 126 DLVRGKAVHLRAEAYGTDCYPRKSLDKKITLSELPYAHLLNPRNCYQNYNAAVNLTSRII 185 DLV K V L+A YGTDCYPRK ++ +ITL ++ A L NPRN YQNYN AVNL+++ I Sbjct: 122 DLVARKKVVLKATGYGTDCYPRKEIETEITLDDINEAILFNPRNAYQNYNCAVNLSTKTI 181 Query: 186 YTYMGPLKPNLRNVNFATAGRISPLFNDPLFRTIGLGTRIFLGGGTGYVLGAGTQHVAAP 245 YTY+G LK NL N +++TAG++SPL DP FRTIG+GTRIFLGGG GYV+ GTQH Sbjct: 182 YTYLGVLKANLGNAHYSTAGQLSPLLKDPQFRTIGVGTRIFLGGGIGYVVWNGTQHFPGR 241 Query: 246 KRTERGLPLSPAG-TLMLKGDLKGMNARYLRGLSFLGYGCSLAVGVGIPIPILNEEIAWF 304 E G AG TL + GDLK M+ R+L G S +GYG +L VG+GIPIP+LNE+I F Sbjct: 242 NLVEDGNDYGYAGATLSVLGDLKQMSPRWLVGTSMIGYGATLTVGIGIPIPVLNEDICRF 301 Query: 305 TGVDDSDIQMPVKDYGHDYPNCLPRVIQHVTYEDLKSGEVEIMGKKVETVPMTSYPLSLE 364 V D ++ P+ DY D+PN + V+Y +LKSG++++ GK+V T P++SYP + E Sbjct: 302 AAVGDDELYAPIMDYSDDFPNLKSNNLGFVSYAELKSGKIKVNGKEVPTAPVSSYPRARE 361 Query: 365 VANTLKSWIEKGEFLLTEPVELLPSA 390 +A TLK WI+KG+FLL EPV+LLP+A Sbjct: 362 IAGTLKQWIQKGDFLLGEPVQLLPNA 387 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: 537 Number of extensions: 27 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: 390 Length of database: 398 Length adjustment: 31 Effective length of query: 359 Effective length of database: 367 Effective search space: 131753 Effective search space used: 131753 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