Align Glycine cleavage system H protein; Octanoyl/lipoyl carrier protein (characterized)
to candidate CA265_RS18980 CA265_RS18980 glycine cleavage system protein H
Query= SwissProt::P64213 (126 letters) >FitnessBrowser__Pedo557:CA265_RS18980 Length = 126 Score = 157 bits (397), Expect = 5e-44 Identities = 71/125 (56%), Positives = 98/125 (78%) Query: 1 MAVPNELKYSKEHEWVKVEGNVATIGITEYAQSELGDIVFVELPETDDEINEGDTFGSVE 60 M P+ELKY+K+HEWVKVEGN A IG+T++AQ ELGDIV+V++ E+ + + FG+VE Sbjct: 1 MNFPSELKYTKDHEWVKVEGNEAIIGVTDFAQRELGDIVYVDINTVGSEVAKEEVFGTVE 60 Query: 61 SVKTVSELYAPISGKVVEVNEELEDSPEFVNESPYEKAWMVKVEISDESQLEALLTAEKY 120 +VKTVS+LY P++G V+EVN EL D+PE VN PY K WMVKV ++D +++E LL+AE Y Sbjct: 61 AVKTVSDLYMPVTGTVLEVNAELNDNPELVNSDPYGKGWMVKVSLADLAEVEDLLSAEAY 120 Query: 121 SEMIG 125 E++G Sbjct: 121 QELVG 125 Lambda K H 0.305 0.127 0.342 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: 78 Number of extensions: 1 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: 126 Length of database: 126 Length adjustment: 14 Effective length of query: 112 Effective length of database: 112 Effective search space: 12544 Effective search space used: 12544 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.0 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