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 WP_012706778.1 NGR_RS12340 ABC transporter permease
Query= uniprot:A0A1N7U128 (237 letters) >NCBI__GCF_000018545.1:WP_012706778.1 Length = 274 Score = 138 bits (347), Expect = 1e-37 Identities = 82/220 (37%), Positives = 122/220 (55%), Gaps = 8/220 (3%) Query: 21 SGVAMTLWLFIISVVLGFFLSIPLALARVSEHVWLRWPVEVYTYLFRGTPLYIQLLICYT 80 SG+ ++L + + +LGF L++PL L +V+ +L+ P ++ + RGTPL +QL + Y Sbjct: 59 SGILVSLAMLFSTAILGFLLAVPLGLVQVTGPWFLKAPARLFCTVIRGTPLLLQLWLLYY 118 Query: 81 GLYSLEI---VQDNALLNQFFRNALNCTLLAFVLNTCAYTVEIFAGAIRNIPHGEIEAAR 137 GL SL ++LL + R A + A L+ AY E+ GA +P GE+EAAR Sbjct: 119 GLGSLFPQFPAIRHSLLWPYLREAWPYGVAALTLSFAAYEGEVMRGAFAGVPQGELEAAR 178 Query: 138 AYGLHGWRLNLFVVVPAALRRALPAYSNEMILMLHATSLAFTATVADILKVARDANAETF 197 AYG+ W + +P A+ RALP + E +L L +T L T TV D+ V ETF Sbjct: 179 AYGMGRWTTFRRIWLPRAVHRALPTLNGETVLQLKSTPLVATITVVDVYAVISKVRQETF 238 Query: 198 LTFQAFGIAALLYMLLSFALVGLFRLAERRWMRFLVPTRG 237 LT++ + AL+Y+ L+ LV FR E R +PTRG Sbjct: 239 LTYEPLLLLALIYLCLTGILVVAFRYFENR-----IPTRG 273 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: 208 Number of extensions: 10 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: 274 Length adjustment: 24 Effective length of query: 213 Effective length of database: 250 Effective search space: 53250 Effective search space used: 53250 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: 47 (22.7 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