Align Homocysteine formation from aspartate semialdehyde (DUF39 component) (characterized)
to candidate WP_011023232.1 MA_RS17210 methanogenesis marker 16 metalloprotein
Query= reanno::Miya:8500721 (390 letters) >NCBI__GCF_000007345.1:WP_011023232.1 Length = 438 Score = 136 bits (342), Expect = 1e-36 Identities = 108/341 (31%), Positives = 158/341 (46%), Gaps = 43/341 (12%) Query: 8 KTIAEINERIRQGKAVVLNAEEMTEAVRRMGKEKAAREIDVVTTGTFSPMCSSGLLFNIG 67 +TI EI +I G+AVVL AEE+ VR G E +IDVVTT T M + +F+ Sbjct: 12 RTIQEIQVKIDAGEAVVLTAEEIGAKVRA-GGEIRLEDIDVVTTATRGIMSGTYAVFSFK 70 Query: 68 QQDPPT-LKTAKVWMNDVPAYAG------LAAVDSYLGATEPTEDDPLNKVYPGRFKYGG 120 +P + +K +KV +N VPA G L +D + T +E D +YGG Sbjct: 71 VSEPDSFVKASKVLLNGVPAIVGPCPNERLGVLDLIVLGTAHSETDS---------RYGG 121 Query: 121 GHVIEDLVRGKAVHLRAEAYGTDCYPRKSLDKKITLSELPYAHLLNPRNCYQNYNAAVNL 180 GH+ D+V GK++ + D + ++ LSE+P+A L R+ ++NY A VN Sbjct: 122 GHLFRDMVEGKSITVDVTTSVGDFFSVET-----RLSEMPFARLYATRHAFKNYRAFVNP 176 Query: 181 TSRIIYTYMG--PLKPNLRNVNFATAGRISPLFNDPLFRTIGLGTRIFLGGGTGYVLGAG 238 I T P + R + F G ++P+ NDP TIG+GTR+ + G G+V G G Sbjct: 177 GKESIKTIFHALPFEGEFRELTFCGCGELNPIQNDPKLETIGIGTRVLINGAEGFVTGQG 236 Query: 239 TQHVAAPKRTERGLPLSPAGTLMLKGDLKGMNARYLRGLSFLGYGCSLAVGVGIPIPILN 298 T R P +P L DL M Y+ G G + +PIP+L+ Sbjct: 237 T----------RSAPDNP--NLTGFADLHDMTPEYMGGF-VTSAGPEIVNTWAVPIPVLS 283 Query: 299 EEIAWFTGVDDSDIQMPVKDYGHDYPNCLPRVIQHVTYEDL 339 E+ DS I + + D P C +TY D+ Sbjct: 284 REMLENILQLDSQIPLKLVDLAGRLPLC------EITYGDV 318 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: 383 Number of extensions: 19 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 390 Length of database: 438 Length adjustment: 31 Effective length of query: 359 Effective length of database: 407 Effective search space: 146113 Effective search space used: 146113 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