Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate 8500829 DvMF_1570 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= uniprot:B2TBJ7 (240 letters) >FitnessBrowser__Miya:8500829 Length = 226 Score = 137 bits (345), Expect = 2e-37 Identities = 74/209 (35%), Positives = 122/209 (58%), Gaps = 11/209 (5%) Query: 18 LLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPELLVIYLF 77 +L +L+TVA A+A+G + G ++ A++ +R++ Y FRG+P L+++ LF Sbjct: 15 ILEGSLVTVATVFGAMALGLLLGVPMSVAQVYGALPVRLVVGFYVWFFRGMPILVLLLLF 74 Query: 78 YFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLAVSRGELEAA 137 YFG + QL G + + F L +GM S AYQ++++R A+LA+ +G+L AA Sbjct: 75 YFG-------LFQLIG----LNLSAFTASCLVLGMTSAAYQSQIFRGAILALPQGQLRAA 123 Query: 138 RSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLRTSQVAAGST 197 R++GM T R I++PQ LR ++PG N + + LKDSAL V G E++ + A T Sbjct: 124 RALGMSDGTAIRSIVLPQALRLSIPGWSNEYSILLKDSALAFVLGTPEIMARTHFVASRT 183 Query: 198 HQYFTFFVVGGALYLIMTSISNRVFNRAE 226 +++ ++ GALY ++T I +V R E Sbjct: 184 YEHLPLYMTAGALYFVITLIGLKVLRRLE 212 Lambda K H 0.327 0.141 0.403 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: 108 Number of extensions: 4 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: 240 Length of database: 226 Length adjustment: 23 Effective length of query: 217 Effective length of database: 203 Effective search space: 44051 Effective search space used: 44051 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: 46 (22.3 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