Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate AZOBR_RS00675 AZOBR_RS00675 ABC transporter permease
Query= uniprot:B2TBJ8 (250 letters) >FitnessBrowser__azobra:AZOBR_RS00675 Length = 229 Score = 222 bits (566), Expect = 4e-63 Identities = 106/226 (46%), Positives = 160/226 (70%) Query: 4 DFDFLFDTIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFR 63 ++D ++D++ LL VP TL L +L+ G ++ + +R+ + + R AY+ VFR Sbjct: 2 NWDLMWDSVPTLLRGVPVTLQLVGLALLFGAGVAFAVALLRLYGNRVTERLMAAYVFVFR 61 Query: 64 GSPLLIQMFLVYYGMGQFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGLMAV 123 G+PLL+Q+FL+YYGMGQF ++R SFLW LREP+ CA+L+L L T YT+EI+RG +++V Sbjct: 62 GTPLLVQIFLIYYGMGQFELVRSSFLWVYLREPFWCAILALTLNTGAYTSEILRGAILSV 121 Query: 124 PVGQIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGV 183 P GQIEA + G+S L RR++ P+A+RQ LPAY E +L+VK+++LAS +T+ E+TG+ Sbjct: 122 PQGQIEAARACGMSRTLLFRRIMMPVAIRQMLPAYGNEVILMVKASSLASTITLLEITGI 181 Query: 184 AQQIIQQTYRTTEVFICAALIYLFLNFVIVRLLGMLETRLSRHLRA 229 A++II Q++ EVFI A IYL LNF+ RL+ E R++ +LRA Sbjct: 182 ARKIIAQSFAVFEVFIVAGSIYLLLNFIASRLIRYAEWRMTPYLRA 227 Lambda K H 0.331 0.143 0.431 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: 172 Number of extensions: 9 Number of successful extensions: 1 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: 250 Length of database: 229 Length adjustment: 23 Effective length of query: 227 Effective length of database: 206 Effective search space: 46762 Effective search space used: 46762 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 (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