Align Glycine cleavage system H protein; Octanoyl/lipoyl carrier protein (characterized)
to candidate WP_008347039.1 BA79_RS04965 glycine cleavage system protein GcvH
Query= SwissProt::O32174 (127 letters) >NCBI__GCF_000691145.1:WP_008347039.1 Length = 127 Score = 232 bits (592), Expect = 1e-66 Identities = 113/127 (88%), Positives = 121/127 (95%) Query: 1 MSIPKDLRYSGEHEWVKVEGEKARIGITHFAQSELGDIVFVELPEVGAEIKADEPFGSVE 60 MS PKDLRYS EHEWVKVEG+K RIGITHFAQSELGDIVFVELPEVG +I ADEPFGSVE Sbjct: 1 MSTPKDLRYSEEHEWVKVEGDKVRIGITHFAQSELGDIVFVELPEVGDKITADEPFGSVE 60 Query: 61 SVKTVSELYAPINGTVVEVNEDLDDSPEFVNESPYEKAWMIVVEPSDASEIEKLMTAEQY 120 SVKTVSELYAPINGT+VEVN++LDDSPEFVN+SPYEKAWMIVVEP+DASEIE LMTAEQY Sbjct: 61 SVKTVSELYAPINGTIVEVNDELDDSPEFVNDSPYEKAWMIVVEPADASEIENLMTAEQY 120 Query: 121 EEMTQED 127 EEMT+ED Sbjct: 121 EEMTKED 127 Lambda K H 0.308 0.129 0.360 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: 143 Number of extensions: 4 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: 127 Length of database: 127 Length adjustment: 14 Effective length of query: 113 Effective length of database: 113 Effective search space: 12769 Effective search space used: 12769 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 24 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