Align Glycine cleavage system H protein (characterized)
to candidate 199966 SO0780 glycine cleavage system H protein (NCBI ptt file)
Query= SwissProt::P0A6T9 (129 letters) >FitnessBrowser__MR1:199966 Length = 129 Score = 206 bits (524), Expect = 9e-59 Identities = 94/129 (72%), Positives = 115/129 (89%) Query: 1 MSNVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAV 60 MSN+P ELKY+ HEW+RKE DG+YTVGITEHAQELLGDMVFV+LPEVG TV+AGDDCAV Sbjct: 1 MSNIPTELKYASSHEWIRKEEDGSYTVGITEHAQELLGDMVFVELPEVGDTVTAGDDCAV 60 Query: 61 AESVKAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDAT 120 AESVKAASDIYAP+SGE++AVN+AL DSPELVNS+ Y GW F++ SDESE+++LLDA Sbjct: 61 AESVKAASDIYAPISGEVIAVNEALEDSPELVNSDAYGEGWFFRVMPSDESEVDALLDAE 120 Query: 121 AYEALLEDE 129 Y+A++++E Sbjct: 121 GYQAVIDEE 129 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: 116 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: 129 Length of database: 129 Length adjustment: 14 Effective length of query: 115 Effective length of database: 115 Effective search space: 13225 Effective search space used: 13225 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