Align ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale)
to candidate BWI76_RS19230 BWI76_RS19230 polar amino acid ABC transporter inner membrane subunit
Query= uniprot:A0A1N7U128 (237 letters) >FitnessBrowser__Koxy:BWI76_RS19230 Length = 241 Score = 182 bits (463), Expect = 4e-51 Identities = 102/227 (44%), Positives = 142/227 (62%), Gaps = 5/227 (2%) Query: 11 AYLFSDGAGL-SGVAMTLWLFIISVVLGFFLSIPLALARVSEHVWLRWPVEVYTYLFRGT 69 ++L+SDG G SG+A+T LF++S+V G L+I +A+ +V L P+ +TY FR T Sbjct: 12 SFLWSDGNGAASGLAVTAELFLLSIVPGMALAIAMAVGQVYGPRGLALPIRAFTYFFRST 71 Query: 70 PLYIQLLICYTGLYSLEIVQDNALLNQ----FFRNALNCTLLAFVLNTCAYTVEIFAGAI 125 PLY+QL++ Y GL +IVQ + +Q FR+A C LA VLNT AY E+ AG + Sbjct: 72 PLYLQLMLIYYGLSQFDIVQTGWMNDQPFWLLFRDATFCATLALVLNTAAYVAELLAGMM 131 Query: 126 RNIPHGEIEAARAYGLHGWRLNLFVVVPAALRRALPAYSNEMILMLHATSLAFTATVADI 185 P E A AYG+ W++ +V+PA LRR +PA +NEM+ +LHATSLA T T+ DI Sbjct: 132 VTFPRQEWIAGEAYGMGKWQIIRRLVLPATLRRGIPALNNEMVFLLHATSLASTVTLLDI 191 Query: 186 LKVARDANAETFLTFQAFGIAALLYMLLSFALVGLFRLAERRWMRFL 232 VAR A T+ F F +AA LY+L +F L+ F AERRW+ F+ Sbjct: 192 TGVARAFYAMTYSPFIPFLMAAALYLLCTFLLIFTFARAERRWLAFI 238 Lambda K H 0.332 0.143 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: 230 Number of extensions: 9 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: 237 Length of database: 241 Length adjustment: 23 Effective length of query: 214 Effective length of database: 218 Effective search space: 46652 Effective search space used: 46652 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 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