Align arginine/ornithine transport protein (characterized)
to candidate BPHYT_RS08555 BPHYT_RS08555 ABC transporter permease
Query= CharProtDB::CH_107317 (229 letters) >FitnessBrowser__BFirm:BPHYT_RS08555 Length = 219 Score = 127 bits (318), Expect = 2e-34 Identities = 75/214 (35%), Positives = 119/214 (55%), Gaps = 12/214 (5%) Query: 9 IVDGAWLTLQLALLSMLLAIVLGLLGAAFRLSPVRWLAWCGDLYATVVRGIPDLVLILLI 68 + GA LT++ A+LSM+ ++ G + A +S R L W +Y +V+RG P LV I +I Sbjct: 14 LAQGAVLTVKFAVLSMIFGLIAGAVLALMGVSHNRVLNWIARIYVSVMRGTPLLVQIFVI 73 Query: 69 FYGGQGLLNWVAPQLGYDDYIDLNPFVSGVGTLGFIFGAYLSETFRGAFMAIPKGQGEAG 128 +YG P G I L+P +GV L AYLSE+ RGA + I GQ A Sbjct: 74 YYG--------LPSFG----ISLDPTPAGVIALSANVAAYLSESMRGAILGIHNGQWLAA 121 Query: 129 YGYGMSHRQVFFRIQVPQMIRLAIPGFTNNWLVLVKATALISVVGLQDMMFKAKQASDAT 188 Y G+S RQ + PQ +R+A+P +N+ + L+K T+L+SV+ + +++ A++ +T Sbjct: 122 YSLGLSRRQTLRYVIAPQALRIAVPSMSNSLISLIKDTSLVSVITVTELLRSAQEIIAST 181 Query: 189 REPFTYYLAVAGLYLLVTSVSLLLLRLLERRYSV 222 +P YLA A +Y ++ V + R ERR ++ Sbjct: 182 YQPLPLYLAAAAVYWVLCQVLESVQRWYERRLAL 215 Lambda K H 0.328 0.144 0.442 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: 96 Number of extensions: 5 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: 229 Length of database: 219 Length adjustment: 22 Effective length of query: 207 Effective length of database: 197 Effective search space: 40779 Effective search space used: 40779 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