Align L-Arginine ABC transporter, permease component 1 (characterized)
to candidate RR42_RS04400 RR42_RS04400 ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_18710 (232 letters) >FitnessBrowser__Cup4G11:RR42_RS04400 Length = 219 Score = 137 bits (344), Expect = 2e-37 Identities = 73/216 (33%), Positives = 120/216 (55%), Gaps = 9/216 (4%) Query: 7 VIYEALPLYFSGLLTTLKLLALSLFFGLLAALPLGLMRVSKQPIVNMTAWLYTYVIRGTP 66 ++ +LP+ G+L T+K LS+ FGL+ + LM +S QP+ A Y ++RGTP Sbjct: 6 LVATSLPVLLQGMLLTIKFALLSMIFGLVLGTVVALMGISHQPVPKAVARAYVSIMRGTP 65 Query: 67 MLVQLFLIYYGLAQFAIVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNG 126 +LVQ+F++YYGL I E T L ++N AY +E + G++ P G Sbjct: 66 LLVQIFVVYYGLPGIGIALEP---------TPAGVLTLSLNVGAYLSESMRGAILGIPRG 116 Query: 127 EIEAAKAMGMSRYKLYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAART 186 + AA ++G+++ + R ++ P ALR A+P SN +I +++ TSL S++T+ ++ A+ Sbjct: 117 QWLAAYSLGLTQGQALRYVIGPQALRLAVPSLSNSLISLIKDTSLVSVITVTELLRTAQE 176 Query: 187 VNAQYYLPFEAYITAGAFYLCLTFILVRLFKLAERR 222 V A Y P Y+ A Y L+ L + +L ERR Sbjct: 177 VIAATYQPLPLYLAVAAIYWMLSTALAHMQRLLERR 212 Lambda K H 0.330 0.140 0.425 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: 106 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: 232 Length of database: 219 Length adjustment: 22 Effective length of query: 210 Effective length of database: 197 Effective search space: 41370 Effective search space used: 41370 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 (21.9 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