Align Homocysteine formation from aspartate semialdehyde (COG2122 or apbE like component) (characterized)
to candidate WP_084057882.1 B9A12_RS10655 UPF0280 family protein
Query= reanno::Miya:8499265 (277 letters) >NCBI__GCF_900176285.1:WP_084057882.1 Length = 244 Score = 152 bits (383), Expect = 9e-42 Identities = 92/235 (39%), Positives = 130/235 (55%), Gaps = 16/235 (6%) Query: 42 VFQVVVEETDLWVTARSGLSGQPGQPVQPDLPDRIAAYVTELRGQIKAWMLLAPDFRTSL 101 VFQV V +TDLW+ A+ LS +P + R Q++ + P F ++ Sbjct: 21 VFQVRVAQTDLWIRAQEDLS-RPAHDL-----------TVTFRRQLEKYAASDPRFLHAM 68 Query: 102 VPVPTPASAPEVARRMAHGADIAGVGPFAAVAGTVAQMVAERFAPVSPDIIVENGGDIYI 161 P+ AP + R M +AGVGP AAVAG +AQ VAE SP ++VENGGD Y+ Sbjct: 69 EPLEDDPLAPPLVRSMLRAGRVAGVGPMAAVAGAIAQAVAEGLVRWSPSVLVENGGDCYL 128 Query: 162 CSQRDRVVGLLPDPASGEMIGVVVK-AADC-PVSLCSSSATIGHSLSLGVGNIAAVRARD 219 S D VV + P S + ++ AAD P ++C+SSA+IGHSLSLG + A V A+D Sbjct: 129 ISAEDLVVSIYPGRNSPFRHSLAIRLAADTFPWAVCTSSASIGHSLSLGRADAATVLAKD 188 Query: 220 ASLADAAATLFGNMLQGPDDVARVTERAAAMAHLGIEGVYAQCGGRVGIWGNMEL 274 A++ADA AT GN ++ P+D+ + H +EG A CG ++ WG +EL Sbjct: 189 AAVADACATALGNRIRRPEDLESAMAWVEGIPH--VEGALAVCGDKLAAWGAVEL 241 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: 157 Number of extensions: 6 Number of successful extensions: 4 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: 244 Length adjustment: 24 Effective length of query: 253 Effective length of database: 220 Effective search space: 55660 Effective search space used: 55660 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