Align Homocysteine formation from aspartate semialdehyde (COG2122 or apbE like component) (characterized)
to candidate WP_027177902.1 G496_RS0102630 UPF0280 family protein
Query= reanno::Miya:8499265 (277 letters) >NCBI__GCF_000429985.1:WP_027177902.1 Length = 247 Score = 218 bits (555), Expect = 1e-61 Identities = 114/252 (45%), Positives = 154/252 (61%), Gaps = 12/252 (4%) Query: 23 HTDHVRGYRKRTARHPDEVVFQVVVEETDLWVTARSGLSGQPGQPVQPDLPDRIAAYVTE 82 ++DH R YRK E FQVVV +TDL++ A S + Q V E Sbjct: 5 YSDHNRAYRKTVKPAKSETSFQVVVAQTDLFIVADKDFSSEALQAVH------------E 52 Query: 83 LRGQIKAWMLLAPDFRTSLVPVPTPASAPEVARRMAHGADIAGVGPFAAVAGTVAQMVAE 142 R +++++LL P+F SLVPV A E+ RRMA + + VGP AAVAG VAQ AE Sbjct: 53 ARALLQSYILLHPEFAESLVPVEVEKDASEIIRRMADSSALCNVGPMAAVAGAVAQFTAE 112 Query: 143 RFAPVSPDIIVENGGDIYICSQRDRVVGLLPDPASGEMIGVVVKAADCPVSLCSSSATIG 202 + A S +++VENGGD Y+ S R VGLL DP SG +G+ ++A D PVS+CSSS IG Sbjct: 113 KLAKQSKEVLVENGGDTYLISSSPRTVGLLSDPESGTKVGLKLEAEDFPVSICSSSGKIG 172 Query: 203 HSLSLGVGNIAAVRARDASLADAAATLFGNMLQGPDDVARVTERAAAMAHLGIEGVYAQC 262 HSLSLG G++ VRA+DA ADAAAT N+L+ P DV V E+A ++ G++G++ Q Sbjct: 173 HSLSLGCGDLVTVRAKDARFADAAATALANLLKSPQDVPLVIEKARQLSESGLDGIFVQF 232 Query: 263 GGRVGIWGNMEL 274 ++G WG +EL Sbjct: 233 DSKIGAWGKIEL 244 Lambda K H 0.319 0.134 0.401 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: 150 Number of extensions: 2 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: 277 Length of database: 247 Length adjustment: 25 Effective length of query: 252 Effective length of database: 222 Effective search space: 55944 Effective search space used: 55944 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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