Align Homocysteine formation from aspartate semialdehyde (DUF39 component) (characterized)
to candidate WP_073041443.1 BUB04_RS16265 hypothetical protein
Query= reanno::Miya:8500721 (390 letters) >NCBI__GCF_900129305.1:WP_073041443.1 Length = 386 Score = 479 bits (1234), Expect = e-140 Identities = 236/385 (61%), Positives = 290/385 (75%), Gaps = 5/385 (1%) Query: 5 KVNKTIAEINERIRQGKAVVLNAEEMTEAVRRMGKEKAAREIDVVTTGTFSPMCSSGLLF 64 +V KT EINERIR+G+AVV+ AEEMT V++MG KAA+E+DVVTTGTF+PMCSSG+ Sbjct: 3 EVKKTYEEINERIRKGQAVVVTAEEMTRIVKKMGPRKAAKEVDVVTTGTFAPMCSSGVFI 62 Query: 65 NIGQQDPPTLKTAKVWMNDVPAYAGLAAVDSYLGATEPTEDDPLNKVYPGRFKYGGGHVI 124 N G PP +K ++VW+NDVPAYAGLAAVD YLGATEPT DDPLNKV+PG F+YGGGHVI Sbjct: 63 NFGHTRPP-IKASRVWLNDVPAYAGLAAVDVYLGATEPTFDDPLNKVHPGTFEYGGGHVI 121 Query: 125 EDLVRGKAVHLRAEAYGTDCYPRKSLDKKITLSELPYAHLLNPRNCYQNYNAAVNLTSRI 184 DLV GK + LRAEAYGTDCYP K ++ +TL +LPYA L NPRN YQNYN AVNL+ + Sbjct: 122 HDLVAGKPIRLRAEAYGTDCYPNKRVEMTVTLDDLPYAVLCNPRNAYQNYNCAVNLSKKT 181 Query: 185 IYTYMGPLKPNLRNVNFATAGRISPLFNDPLFRTIGLGTRIFLGGGTGYVLGAGTQHVAA 244 IYTYMG LKP+L N N++T+G +SPL NDP +RT+GLGTRIFLGG GYV+ G+QH Sbjct: 182 IYTYMGTLKPSLGNANYSTSGELSPLLNDPYYRTLGLGTRIFLGGAQGYVVWHGSQHNPN 241 Query: 245 PKRTERGLPLSPAGTLMLKGDLKGMNARYLRGLSFLGYGCSLAVGVGIPIPILNEEIAWF 304 R G+P PAGTLM+ GDLK M+ R+L G+S GYGCSLAVG+G+PIPIL+EE+A F Sbjct: 242 APRLPNGVPRMPAGTLMVLGDLKEMDPRWLLGVSIQGYGCSLAVGIGVPIPILDEEMAAF 301 Query: 305 TGVDDSDIQMPVKDYGHDYPNCLPRVIQHVTYEDLKSGEVEIMGKKVETVPMTSYPLSLE 364 TGV D++I VKDY L V YE+L+SG + + GK V TVP++S + E Sbjct: 302 TGVSDAEIVTQVKDYSFTQSEPL----AEVNYEELRSGTIRVAGKDVPTVPLSSVVRARE 357 Query: 365 VANTLKSWIEKGEFLLTEPVELLPS 389 +A LK+WIE+G F L P +LLPS Sbjct: 358 IAGILKTWIEEGRFELGVPQKLLPS 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: 556 Number of extensions: 21 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: 386 Length adjustment: 30 Effective length of query: 360 Effective length of database: 356 Effective search space: 128160 Effective search space used: 128160 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