Align ABC transporter for D-mannitol and D-mannose, permease component 1 (characterized)
to candidate WP_011842345.1 RSPH17029_RS17170 sugar ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_25885 (308 letters) >NCBI__GCF_000015985.1:WP_011842345.1 Length = 308 Score = 130 bits (326), Expect = 5e-35 Identities = 89/284 (31%), Positives = 146/284 (51%), Gaps = 8/284 (2%) Query: 3 TSTLKAQMDIPAPLRKSRLANP--GWFLVSPSVALLLLWMIVPLGMTLYFSLIRYNLLYP 60 TS + D AP R++RL L+SP+V + L + P+ T + SL Y L P Sbjct: 2 TSVPVSDRDEIAPARRARLWRQVLPLALLSPAVLVTLAIVFFPMVQTAWMSLHDYVLFRP 61 Query: 61 GDNAFVGLENFSYFLTDSGFLPGATNTLLLVGSVLLISVVFGVLISALLEASEFLGRGIV 120 +VGL++++ L D F +T+L + + + G L +ALL +F R + Sbjct: 62 KKFDWVGLKHYAAILQDEVFWISLRHTVLWIAITVPAQALLG-LATALLLNQKFPWRPVA 120 Query: 121 RVMLISPFFIMPTVGALIWKNLIFHPVSGILAAVWKLFGA--QPVDWLAH--YPLLSIII 176 R ++I P+ + V AL+W I+ G+L + G Q + WLA+ L +II+ Sbjct: 121 RALIIIPWALPSVVIALMWA-WIYDSNYGVLNDLLLRVGILEQSIPWLANPGTALYAIIL 179 Query: 177 IVSWQWLPFAILILMTAMQSLDQEQKEAARLDGAGPIAIFWHLTLPHLARPIAVVVMIET 236 ++WQ PF ++++ +QS+ + EAA LDGA + FWH+TLP ++ + +++ T Sbjct: 180 TLTWQGFPFFAVMILAGLQSIPRSYYEAASLDGASSLRQFWHITLPGISGVLFTAILLRT 239 Query: 237 IFLLSVFAEIFTTTNGGPGYASTNLAYLIYNQALVQFDVGMASA 280 I++ + IF T GGPGYA+ L + +A D G SA Sbjct: 240 IWVANSMDVIFVMTGGGPGYATYTLPLYAFLEARTNLDFGYGSA 283 Lambda K H 0.328 0.142 0.433 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: 309 Number of extensions: 21 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: 308 Length of database: 308 Length adjustment: 27 Effective length of query: 281 Effective length of database: 281 Effective search space: 78961 Effective search space used: 78961 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 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