Align Glycine cleavage system H protein (characterized)
to candidate 3609295 Dshi_2681 glycine cleavage system H protein (RefSeq)
Query= SwissProt::Q5SKW9 (128 letters) >FitnessBrowser__Dino:3609295 Length = 122 Score = 127 bits (318), Expect = 7e-35 Identities = 59/117 (50%), Positives = 80/117 (68%) Query: 8 FYTKTHEWALPEGDTVLVGITDYAQDALGDVVYVELPEVGRVVEKGEAVAVVESVKTASD 67 +YT HEW E DT +GIT +A + LG+VV++EL G KG+ + VVESVK ASD Sbjct: 5 YYTDDHEWIEVEDDTATIGITKHAAEQLGEVVFIELQPEGETFVKGDEIGVVESVKAASD 64 Query: 68 IYAPVAGEIVEVNLALEKTPELVNQDPYGEGWIFRLKPRDMGDLDELLDAGGYQEVL 124 I+APV GEI+E N AL +TP +N+DP G W++++K D G+L ELLDA GY ++ Sbjct: 65 IFAPVTGEILEANAALVETPAELNEDPEGNSWLYKIKLSDPGELSELLDAEGYAALI 121 Lambda K H 0.313 0.137 0.394 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: 73 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: 128 Length of database: 122 Length adjustment: 14 Effective length of query: 114 Effective length of database: 108 Effective search space: 12312 Effective search space used: 12312 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.4 bits) S2: 41 (20.4 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