Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, 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::Q9HU29 (230 letters) >FitnessBrowser__Miya:8500829 Length = 226 Score = 145 bits (365), Expect = 8e-40 Identities = 82/218 (37%), Positives = 134/218 (61%), Gaps = 8/218 (3%) Query: 7 ILKWMPKMLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFRGTPL 66 I++ +P +L+G+ +T+ + A+ GL L +P+ +A+ VR V Y++FFRG P+ Sbjct: 8 IIEALPYILEGSLVTVATVFGAMALGLLLGVPMSVAQVYGALPVRLVVGFYVWFFRGMPI 67 Query: 67 LLQLFIVYYGLAQFEEVRKSAFWPYLRDPYWCALLTMTLHTAAYIAEILRGAIHSVPVGE 126 L+ L + Y+GL Q + SAF C +L MT +AAY ++I RGAI ++P G+ Sbjct: 68 LVLLLLFYFGLFQLIGLNLSAFTAS------CLVLGMT--SAAYQSQIFRGAILALPQGQ 119 Query: 127 VEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMGMARTI 186 + AARALGMS A+ I+LP+A+R+ +P +SNE ++LK SA+ + + +IM + Sbjct: 120 LRAARALGMSDGTAIRSIVLPQALRLSIPGWSNEYSILLKDSALAFVLGTPEIMARTHFV 179 Query: 187 IARTYESMLFFCLAGALYLVITIVLTRIFRLIERWLRV 224 +RTYE + + AGALY VIT++ ++ R +E L + Sbjct: 180 ASRTYEHLPLYMTAGALYFVITLIGLKVLRRLEHKLHI 217 Lambda K H 0.332 0.142 0.443 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: 158 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: 230 Length of database: 226 Length adjustment: 23 Effective length of query: 207 Effective length of database: 203 Effective search space: 42021 Effective search space used: 42021 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (22.0 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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