Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate RR42_RS29445 RR42_RS29445 ABC transporter permease
Query= uniprot:A0A159ZYE0 (418 letters) >FitnessBrowser__Cup4G11:RR42_RS29445 Length = 358 Score = 158 bits (400), Expect = 2e-43 Identities = 103/320 (32%), Positives = 166/320 (51%), Gaps = 35/320 (10%) Query: 98 LIVGALVWPFFGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYAL 157 L+ L+ P + S + +LIY + GLGL ++ G GLL +G+ F VGAY+ A Sbjct: 28 LMACLLIAPGWASSYWIAQLGFVLIYAIAGLGLMVLSGYTGLLSIGHAAFLGVGAYTQAW 87 Query: 158 LSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDI 217 L+ + G+ F L A ++A G ++G P LR++G YLAI TL FG I+ L + Sbjct: 88 LTSH-GVPFVPALLAAAALSALTGVVVGLPALRVKGIYLAIATLAFGLIVEEILARWESV 146 Query: 218 TGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAAL 277 TGG G+ + P +G + V F YL + LA L Sbjct: 147 TGGNAGLP-VAAPQLWGYVLD---------------------GPVAFYYLSLAVCLLATL 184 Query: 278 FVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGL 337 V+N LLR GRA+ A+R+ EI+ +++G++ K +F L AA G AG+ +A + Sbjct: 185 AVLN-LLRSATGRAFIAIRDSEISAQSMGIHLARYKTLSFALSAALVGIAGALYAHKLRY 243 Query: 338 VTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEM-----------MREFSEY 386 ++PE F +S +L +VV+GG+GS G L AI +I++P+M + + S Sbjct: 244 ISPEQFGIAQSIDLLLLVVVGGLGSVHGAFLGAIFLIVMPQMIVLAKDLLPPAIGQASGM 303 Query: 387 RMLMFGALMVLMMIWRPQGL 406 + L++G +++ +++ P GL Sbjct: 304 QALVYGLVLMAFVLFEPMGL 323 Lambda K H 0.331 0.145 0.439 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: 424 Number of extensions: 25 Number of successful extensions: 5 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: 418 Length of database: 358 Length adjustment: 30 Effective length of query: 388 Effective length of database: 328 Effective search space: 127264 Effective search space used: 127264 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: 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