Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate RR42_RS34785 RR42_RS34785 ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__Cup4G11:RR42_RS34785 Length = 287 Score = 167 bits (422), Expect = 3e-46 Identities = 99/295 (33%), Positives = 160/295 (54%), Gaps = 18/295 (6%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 M F+QQ+LNGLTLG +Y LVA+G T+VYGI+ + NFAHG +M G + + + ++TS+ Sbjct: 1 MTLFLQQVLNGLTLGGVYSLVALGLTLVYGILHVPNFAHGAFYMAGAYVS---YYLMTSL 57 Query: 61 FAGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQ 120 +A+ + V + M + +R+ + PLR + L +I AIG+ + L Q Sbjct: 58 GMNYWLAMGAAAIAVAVLSMLA------DRLVFHPLRNAPELHDMIAAIGIMLFLEAGAQ 111 Query: 121 VTQGPRNKPIPPMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATE 180 G +P + + +S ++++II L+ + + RT G A Sbjct: 112 AMWGADFHRMPTPYGQMVEVMGLSAPAQRLLIIAAAFGLMVLLHLFLTRTVTGSTIVAMA 171 Query: 181 QDRKMAALLGVNVDQTISITFVMGAALAAVAGTMY----LMYYGVASFNDGFTPGVKAFT 236 Q+R+ AAL+G++ + + F + ALAA+A T+Y L+Y + G KAF Sbjct: 172 QNREGAALVGIDATRVTLLVFAISGALAAIAATLYAPINLVYPSM-----GNLVITKAFV 226 Query: 237 AAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGI 291 +LGG+GS+PGA+ GGL+IG+ ES Y + YKD+ FA+L +L +P G+ Sbjct: 227 IIILGGMGSIPGAIVGGLIIGMAESFGGFYVSTDYKDIIAFALLVLILSIRPQGL 281 Lambda K H 0.329 0.143 0.421 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: 261 Number of extensions: 14 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: 300 Length of database: 287 Length adjustment: 26 Effective length of query: 274 Effective length of database: 261 Effective search space: 71514 Effective search space used: 71514 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