Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate GFF2660 PS417_13560 nickel permease
Query= uniprot:B2TBJ8 (250 letters) >FitnessBrowser__WCS417:GFF2660 Length = 232 Score = 150 bits (378), Expect = 3e-41 Identities = 86/206 (41%), Positives = 123/206 (59%), Gaps = 4/206 (1%) Query: 21 TTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRGSPLLIQMFLVYYGMG- 79 TTL L S +LG L++++ R+S R A+AY V RG+PLLIQ+++ YYG+G Sbjct: 18 TTLSLLVISALLGFALAVLVALARLSRRKWLARGAQAYTSVLRGTPLLIQIYIFYYGLGS 77 Query: 80 ---QFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGLMAVPVGQIEAGYSIGL 136 QF +IR SFLWP LR+ Y V +L L Y E+IRGGL+AVP G++EA + G+ Sbjct: 78 LFAQFPMIRGSFLWPYLRDGYWYIVFALVLSVGAYVGEVIRGGLLAVPKGEMEAASAFGM 137 Query: 137 SGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGVAQQIIQQTYRTTE 196 + L RV P A+R LP + E V+L+KSTALAS + V ++ G A + QT + + Sbjct: 138 TPRQALLRVRLPRAMRLLLPTLAGETVMLLKSTALASTIAVVDLLGAANVVRAQTLQIYQ 197 Query: 197 VFICAALIYLFLNFVIVRLLGMLETR 222 + A +YL L F+I + + E R Sbjct: 198 PLLLVAAVYLCLTFLIEGVYAIAERR 223 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: 160 Number of extensions: 8 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: 250 Length of database: 232 Length adjustment: 23 Effective length of query: 227 Effective length of database: 209 Effective search space: 47443 Effective search space used: 47443 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