Align Glycine cleavage system H protein (characterized)
to candidate Pf6N2E2_5559 Glycine cleavage system H protein
Query= SwissProt::Q5SKW9 (128 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5559 Length = 127 Score = 125 bits (313), Expect = 3e-34 Identities = 61/121 (50%), Positives = 85/121 (70%), Gaps = 2/121 (1%) Query: 9 YTKTHEWALPEGD-TVLVGITDYAQDALGDVVYVELPEVGRVVEKGEAVAVVESVKTASD 67 +T+ HEW E D ++ VGIT +AQ+ALGDVVYV+LPE+ + +KG + VESVK AS Sbjct: 6 FTEDHEWLRTEADGSITVGITAFAQNALGDVVYVQLPEL-QSYDKGAEASTVESVKAASG 64 Query: 68 IYAPVAGEIVEVNLALEKTPELVNQDPYGEGWIFRLKPRDMGDLDELLDAGGYQEVLESE 127 +Y P+ GE++EVN ALE PELVN+DP G+GW FR KP + + +LLD Y ++++ Sbjct: 65 VYMPLDGEVLEVNPALESNPELVNEDPLGDGWFFRFKPVNAAAVGQLLDQDAYDRLIKAN 124 Query: 128 A 128 A Sbjct: 125 A 125 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: 65 Number of extensions: 3 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: 128 Length of database: 127 Length adjustment: 14 Effective length of query: 114 Effective length of database: 113 Effective search space: 12882 Effective search space used: 12882 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