Align Glycine cleavage system H protein (characterized)
to candidate Dsui_2736 Dsui_2736 glycine cleavage system H protein
Query= SwissProt::P0A6T9 (129 letters) >FitnessBrowser__PS:Dsui_2736 Length = 128 Score = 164 bits (416), Expect = 3e-46 Identities = 75/129 (58%), Positives = 105/129 (81%), Gaps = 1/129 (0%) Query: 1 MSNVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAV 60 MSNVPA+LKY+K HEW+R EADG+ TVGIT+HAQE LGD+VF++LPEVG T++AG + AV Sbjct: 1 MSNVPADLKYTKSHEWVRLEADGSVTVGITDHAQEALGDLVFIELPEVGKTLAAGQEAAV 60 Query: 61 AESVKAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDAT 120 ESVKAA+D+YAP++G + AVN+A+ D+PE +N + YA W+FK++ ++ +L +LLDA Sbjct: 61 VESVKAAADVYAPIAGSVTAVNEAVVDAPETLNQDAYA-AWLFKLQPANAGDLGALLDAA 119 Query: 121 AYEALLEDE 129 AY A+ + E Sbjct: 120 AYGAVADSE 128 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: 86 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: 129 Length of database: 128 Length adjustment: 14 Effective length of query: 115 Effective length of database: 114 Effective search space: 13110 Effective search space used: 13110 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: 41 (21.2 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