Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate GFF137 Psest_0137 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= uniprot:B2TBJ8 (250 letters) >FitnessBrowser__psRCH2:GFF137 Length = 231 Score = 98.2 bits (243), Expect = 1e-25 Identities = 66/213 (30%), Positives = 103/213 (48%), Gaps = 2/213 (0%) Query: 15 LLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRGSPLLIQMFLV 74 L+A T+ L SL LG +L L+ + SP+ Y + RG P L+ + L+ Sbjct: 12 LIAGTWMTIQLALASLALGLVLGLLGALAKTSPYSALRWLGGTYSTIVRGVPELLWVLLI 71 Query: 75 YYG-MGQFGVIRESF-LWPVLREPYMCAVLSLALCTAGYTAEIIRGGLMAVPVGQIEAGY 132 Y+G + I E F + + P+ ++L LC Y E+ RG L+A+P G EAG Sbjct: 72 YFGTISMIRGIGELFGIENLALSPFAAGTIALGLCFGAYATEVFRGALLAIPKGHREAGL 131 Query: 133 SIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGVAQQIIQQTY 192 ++GL + R+I P R LP ++L+K TAL S++ + E+ +Q + + Sbjct: 132 ALGLGKRRIFTRLILPQMWRLALPGLGNLFMILMKDTALVSVIGLEEIMRRSQIAVTASK 191 Query: 193 RTTEVFICAALIYLFLNFVIVRLLGMLETRLSR 225 F+ AA IYL L V + + LE R R Sbjct: 192 EPFTFFLVAAFIYLCLTIVAMVGMHFLEKRAGR 224 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: 154 Number of extensions: 9 Number of successful extensions: 3 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: 231 Length adjustment: 23 Effective length of query: 227 Effective length of database: 208 Effective search space: 47216 Effective search space used: 47216 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 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