Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate SM_b21137 SM_b21137 amino acid ABC transporter permease
Query= uniprot:Q31RN9 (396 letters) >FitnessBrowser__Smeli:SM_b21137 Length = 219 Score = 112 bits (280), Expect = 1e-29 Identities = 66/203 (32%), Positives = 117/203 (57%), Gaps = 8/203 (3%) Query: 190 GLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLP-LVTILFFGQV 248 GL ++++ +L+S+V LG+ + L ++W+ Y + RG P LV +L V Sbjct: 19 GLGVSVSISLLSIVVGTVLGVFVGLALVYGFRPVKWIVRGYTDFIRGTPVLVLVLASYYV 78 Query: 249 MVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALGLNLFQTY 308 + + +D + ++ L +F S+++ E VRG LQ+IP+GQ EAA A+GL QT+ Sbjct: 79 LSTIGID----LGPFQAGVLALAVFCSSHVGELVRGALQSIPKGQTEAAKAIGLTFAQTF 134 Query: 309 RFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYLGRYAEVYL 368 +++ PQALR ++PA V +++ +TLLSI+G+ ELL ++ +++ E Y Sbjct: 135 TYVLGPQALRQALPAWVNTAAEMVKASTLLSIIGVSELLLRTQELISRTF---MSLEFYF 191 Query: 369 FLGVLYWLCCYGLAQLSRRLEQR 391 F G LY++ YG+ + R +E++ Sbjct: 192 FAGFLYFVINYGIERFGRYVERK 214 Lambda K H 0.329 0.142 0.471 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: 204 Number of extensions: 10 Number of successful extensions: 3 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: 396 Length of database: 219 Length adjustment: 26 Effective length of query: 370 Effective length of database: 193 Effective search space: 71410 Effective search space used: 71410 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 (21.8 bits) S2: 48 (23.1 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