Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate Pf6N2E2_3920 Cystine ABC transporter, permease protein
Query= uniprot:B2TBJ8 (250 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3920 Length = 221 Score = 126 bits (316), Expect = 4e-34 Identities = 79/217 (36%), Positives = 115/217 (52%), Gaps = 9/217 (4%) Query: 10 DTIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRGSPLLI 69 D+ LL T+ L + G LL + MR+S L N AR Y+ FRG+PLL+ Sbjct: 10 DSAPFLLKGAYYTVFLSLGGMFFGLLLGFGLALMRLSRFKLVNWIARIYVSFFRGTPLLV 69 Query: 70 QMFLVYYGMGQFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGLMAVPVGQIE 129 Q+F++YYG+ Q G+ + P A++ +L A Y EI+R + ++ GQ E Sbjct: 70 QLFVIYYGLPQLGIELD---------PLPAALIGFSLNMAAYACEILRAAISSIERGQWE 120 Query: 130 AGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGVAQQIIQ 189 A SIG++ LRR I P A R LP + LVK TALA+ + V E+ AQ I Sbjct: 121 AAASIGMTRAQTLRRAILPQAARTALPPLGNSFISLVKDTALAATIQVPELFRQAQLITA 180 Query: 190 QTYRTTEVFICAALIYLFLNFVIVRLLGMLETRLSRH 226 +T+ +++ AALIY L V+ L +LE R++RH Sbjct: 181 RTFEIFTMYLAAALIYWVLATVLSHLQNVLEARVNRH 217 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: 130 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: 250 Length of database: 221 Length adjustment: 23 Effective length of query: 227 Effective length of database: 198 Effective search space: 44946 Effective search space used: 44946 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