Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate 5209440 Shew_1911 hypothetical protein (RefSeq)
Query= TCDB::Q8J305 (216 letters) >FitnessBrowser__PV4:5209440 Length = 213 Score = 143 bits (361), Expect = 2e-39 Identities = 80/213 (37%), Positives = 128/213 (60%), Gaps = 8/213 (3%) Query: 2 LEVVEFLKYLILLYGGLFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVVF 61 L++ ++K+ + GL AI NP+G +PVF+S+T + ER +VV L+V Sbjct: 3 LDLTLYVKFFL----GLVAIINPIGLLPVFVSLTSHQTEAERNHTGKVANFAVVVILLVT 58 Query: 62 ALLGQWIFKFFGSSTDAFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVTLEE 121 + GQ I F S AF IAGG L+ +A+ ML GKL VK + EE E S +E Sbjct: 59 IIAGQHILNMFSISLSAFRIAGGTLIAIIAMSMLQGKLGEVKRNQEEDREASG----MES 114 Query: 122 VAIIPLAIPLISGPGAITTVMLYMAKSTTNLQRLAVILTIILIGITVWFVLCSANRIKAR 181 VA++PLA+PL++GPGAI++V++ A+ T + + +T+++ G+T + + A I Sbjct: 115 VAVVPLALPLMAGPGAISSVIVSAAQHNTFSDLIGMSITVVIFGLTSFTLFRMAPVIFKL 174 Query: 182 LGRVGIKVMTRMMGLILTSMAVQMIINGIKGAF 214 LG+ GI V+TR+MGL++ S+ ++++ G KG F Sbjct: 175 LGKTGINVITRLMGLLMLSIGIEVMAAGFKGLF 207 Lambda K H 0.327 0.141 0.396 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: 112 Number of extensions: 6 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: 216 Length of database: 213 Length adjustment: 22 Effective length of query: 194 Effective length of database: 191 Effective search space: 37054 Effective search space used: 37054 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 45 (21.9 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