Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate RR42_RS34785 RR42_RS34785 ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >FitnessBrowser__Cup4G11:RR42_RS34785 Length = 287 Score = 201 bits (511), Expect = 2e-56 Identities = 109/283 (38%), Positives = 173/283 (61%), Gaps = 2/283 (0%) Query: 1 MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMN 60 M L LQQ++NGL LG VY+L+ALG T+VYGI+ + NFAHG YM GA++ Y+L+ S MN Sbjct: 1 MTLFLQQVLNGLTLGGVYSLVALGLTLVYGILHVPNFAHGAFYMAGAYVSYYLMTSLGMN 60 Query: 61 FFVALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRA 120 +++A+ A +A A+L ++ + L + PLR++ + +I AIG+ LE G + GA+ Sbjct: 61 YWLAMGAAAIAVAVLSMLADRLVFHPLRNAPELHDMIAAIGIMLFLEAGAQAMWGADFHR 120 Query: 121 FPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQL 180 P + +G +S +L+I+ + LM+LL + + +T G + A++ + + A L Sbjct: 121 MPTPYGQMVEVMG-LSAPAQRLLIIAAAFGLMVLLHLFLTRTVTGSTIVAMAQNREGAAL 179 Query: 181 MGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPG 240 +GI+ R FA+ ALA A L A N + P MG K+FV +LGG+G IPG Sbjct: 180 VGIDATRVTLLVFAISGALAAIAATLYA-PINLVYPSMGNLVITKAFVIIILGGMGSIPG 238 Query: 241 AALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGI 283 A +GG +IG+ E+F + +D++D I + +L+LIL +RP G+ Sbjct: 239 AIVGGLIIGMAESFGGFYVSTDYKDIIAFALLVLILSIRPQGL 281 Lambda K H 0.330 0.146 0.407 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: 198 Number of extensions: 6 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: 292 Length of database: 287 Length adjustment: 26 Effective length of query: 266 Effective length of database: 261 Effective search space: 69426 Effective search space used: 69426 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 (21.8 bits) S2: 48 (23.1 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