Align Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate 8500829 DvMF_1570 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::Q9HU30 (231 letters) >FitnessBrowser__Miya:8500829 Length = 226 Score = 133 bits (334), Expect = 3e-36 Identities = 77/210 (36%), Positives = 118/210 (56%), Gaps = 10/210 (4%) Query: 12 LLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPETLWVLMI 71 +L G+ +T+ A+ +GLLLG+ ++A+ +R + G Y RG+P + +L+ Sbjct: 15 ILEGSLVTVATVFGAMALGLLLGVPMSVAQVYGALPVRLVVGFYVWFFRGMPILVLLLLF 74 Query: 72 YFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALLSIPRGHREAGQ 131 YFG LF L LS F A L LG+ AY +++FRGA+L++P+G A + Sbjct: 75 YFG----------LFQLIGLNLSAFTASCLVLGMTSAAYQSQIFRGAILALPQGQLRAAR 124 Query: 132 ALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQVASNATK 191 ALG+S G IVLPQ R+++PG N Y ILLKD+AL ++ EIM + ++ T Sbjct: 125 ALGMSDGTAIRSIVLPQALRLSIPGWSNEYSILLKDSALAFVLGTPEIMARTHFVASRTY 184 Query: 192 EPFTFYMTAAAIYLSLTVVIMVALHFLERR 221 E YMTA A+Y +T++ + L LE + Sbjct: 185 EHLPLYMTAGALYFVITLIGLKVLRRLEHK 214 Lambda K H 0.327 0.143 0.431 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: 133 Number of extensions: 7 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 231 Length of database: 226 Length adjustment: 23 Effective length of query: 208 Effective length of database: 203 Effective search space: 42224 Effective search space used: 42224 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