Align Homocysteine formation from aspartate semialdehyde (COG2122 or apbE like component) (characterized)
to candidate WP_018123723.1 B149_RS0103210 UPF0280 family protein
Query= reanno::Miya:8499265 (277 letters) >NCBI__GCF_000375485.1:WP_018123723.1 Length = 248 Score = 228 bits (580), Expect = 1e-64 Identities = 128/253 (50%), Positives = 159/253 (62%), Gaps = 12/253 (4%) Query: 22 VHTDHVRGYRKRTARHPDEVVFQVVVEETDLWVTARSGLSGQPGQPVQPDLPDRIAAYVT 81 +H+D R YR A +EV FQV VE+TDL V AR LS + +A V+ Sbjct: 4 IHSDPNRRYRDSVAPSGNEVRFQVAVEQTDLLVVAREDLSRE------------VAGVVS 51 Query: 82 ELRGQIKAWMLLAPDFRTSLVPVPTPASAPEVARRMAHGADIAGVGPFAAVAGTVAQMVA 141 LRG IK +L P+F SLVPV SAPE+ R MA G+ GVGP AAVAGTVA+ VA Sbjct: 52 GLRGSIKNHILFHPEFAESLVPVEVTDSAPEIVRAMATGSAPCGVGPMAAVAGTVAEFVA 111 Query: 142 ERFAPVSPDIIVENGGDIYICSQRDRVVGLLPDPASGEMIGVVVKAADCPVSLCSSSATI 201 FA SPDIIVENGGDI++ S R+RVV LLPDP SG IG+ + P+S+CSSSATI Sbjct: 112 REFATRSPDIIVENGGDIFMHSTRERVVALLPDPESGASIGIRLTCDRFPLSVCSSSATI 171 Query: 202 GHSLSLGVGNIAAVRARDASLADAAATLFGNMLQGPDDVARVTERAAAMAHLGIEGVYAQ 261 GHSLSLG G + V A+ +LADAAAT NML+ + + A ++ G+EGV+AQ Sbjct: 172 GHSLSLGAGELVTVAAKSGALADAAATALCNMLRNRSSINMLLAEAERLSAYGLEGVFAQ 231 Query: 262 CGGRVGIWGNMEL 274 G+V WG +EL Sbjct: 232 VDGQVAAWGEVEL 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: 213 Number of extensions: 7 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: 248 Length adjustment: 25 Effective length of query: 252 Effective length of database: 223 Effective search space: 56196 Effective search space used: 56196 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