Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate RR42_RS00200 RR42_RS00200 ABC transporter permease
Query= SwissProt::P22729 (425 letters) >FitnessBrowser__Cup4G11:RR42_RS00200 Length = 376 Score = 159 bits (401), Expect = 2e-43 Identities = 95/289 (32%), Positives = 159/289 (55%), Gaps = 14/289 (4%) Query: 119 MIYIILGLGLNVVVGLSGLLVLGYGGFYAIGAYTFALLNHYYGLGFWTCLPIAGLMAAAA 178 ++Y LGL + G SG+ F+ IG+Y A++ + G+ + I+G++AA Sbjct: 89 LLYTTACLGLTLQFGFSGVANFAGAAFFGIGSYATAVMAMHTGIPHLLIIVISGVIAALV 148 Query: 179 GFLLGFPVLRLRGDYLAIVTLGFGEIVRILLLNNTEITGGPNGISQIPKPTLFGLEFSRT 238 G +L PVLR RG Y A+VT+ FG + + + N ++ GGP G+ Q+P T+FG + Sbjct: 149 GSMLITPVLRTRGHYAALVTIAFGILFKTFIEVN-DVLGGPQGL-QVPGMTIFGYALNDG 206 Query: 239 AREGGWDTFSNFFGLKYDPSDRVIFLYLVALLLVVLSLFVINRLLRMPLGRAWEALREDE 298 G D +F+ + L++L + + L R +G + + +R DE Sbjct: 207 FTVAGVDV--SFY----------VSYALISLGICAGVFATVKALERSWVGLSMDVVRTDE 254 Query: 299 IACRSLGLSPRRIKLTAFTISAAFAGFAGTLFAARQGFVSPESFTFAESAFVLAIVVLGG 358 A + GL R K+ AF + FAG AG+++ GFV+P +FTF++S +L+IV+LGG Sbjct: 255 TAAATFGLHIARWKVVAFMLGNFFAGIAGSMYGMITGFVAPNNFTFSDSLLMLSIVILGG 314 Query: 359 MGSQFAVILAAILLVVSRELMRDFNEYSMLMLGGLMVLMMIWRPQGLLP 407 +G+ +I AAI+++V E ++ EY L L++ ++++RP GLLP Sbjct: 315 LGNAVGLIPAAIIVLVLPEKLQFIQEYRFLFYAALVIAILLFRPDGLLP 363 Lambda K H 0.330 0.145 0.436 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: 308 Number of extensions: 12 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: 425 Length of database: 376 Length adjustment: 31 Effective length of query: 394 Effective length of database: 345 Effective search space: 135930 Effective search space used: 135930 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: 50 (23.9 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