Align Glycine cleavage system H protein (characterized)
to candidate GFF4052 Psest_4125 Glycine cleavage system H protein (lipoate-binding)
Query= SwissProt::P0A6T9 (129 letters) >FitnessBrowser__psRCH2:GFF4052 Length = 154 Score = 82.8 bits (203), Expect = 2e-21 Identities = 40/106 (37%), Positives = 62/106 (58%), Gaps = 1/106 (0%) Query: 5 PAELKYSKEHE-WLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAVAES 63 P L+Y+ EH WLR+E DG+ T+G+T + L G + VGA + V E Sbjct: 9 PDALRYAPEHSLWLREEVDGSVTLGLTAYGCALYGQIFAFTPKRVGARIERERSFGVVEF 68 Query: 64 VKAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASD 109 KAAS +P++GE++AVN+AL + P L+N + Y GW+ +++ D Sbjct: 69 AKAASSARSPLAGELLAVNEALLERPALINQDCYGDGWLVRLRPED 114 Lambda K H 0.308 0.127 0.354 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: 58 Number of extensions: 3 Number of successful extensions: 1 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: 129 Length of database: 154 Length adjustment: 15 Effective length of query: 114 Effective length of database: 139 Effective search space: 15846 Effective search space used: 15846 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.6 bits) S2: 42 (20.8 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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