Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate 8502039 DvMF_2752 inner-membrane translocator (RefSeq)
Query= uniprot:A0A159ZYE0 (418 letters) >FitnessBrowser__Miya:8502039 Length = 330 Score = 220 bits (560), Expect = 6e-62 Identities = 126/325 (38%), Positives = 183/325 (56%), Gaps = 26/325 (8%) Query: 85 LTLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGY 144 +T+ T + +A++V L P D+ I +Y +L L LNI++G AGL +G+ Sbjct: 1 MTVSRTTSYAGIAVVVAVL--PLLLDPYWTDVFVSIGLYSVLALSLNIILGQAGLFHMGH 58 Query: 145 VGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFG 204 FYAVGAY A+ + +G+ +P AG+ AA F ++ P++ LRGDYL IVT+G Sbjct: 59 AAFYAVGAYVTAIANTMWGVPVLWAMPFAGLAAALFAMVVARPIIHLRGDYLLIVTIGIV 118 Query: 205 EIIRL-FLRNLTDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVI 263 EI+R+ + N+ +TGG NGI I +P FG I K + Sbjct: 119 EIVRIALINNVFGLTGGANGIFGISRPMLFGF----------------------KIAKPV 156 Query: 264 FLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAF 323 Y + ++ + RL GRA ++ED+ A G+N KL AF LGA + Sbjct: 157 HFYYLVWAYVACSILLFRRLENSRFGRALNYIKEDDTAAEGSGVNIASYKLWAFVLGAFW 216 Query: 324 AGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEMMREF 383 AG G+ +AA+ +++PESF+F ES ++ AIV+LGG GS GV+L A ++I LPE REF Sbjct: 217 AGMTGTIYAAKMTIISPESFSFWESVVLFAIVILGG-GSNRGVLLGAFLLIGLPEFFREF 275 Query: 384 SEYRMLMFGALMVLMMIWRPQGLLP 408 + RML FG MV+MMI+RPQG+LP Sbjct: 276 ASARMLAFGLAMVVMMIFRPQGMLP 300 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: 433 Number of extensions: 17 Number of successful extensions: 4 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: 330 Length adjustment: 30 Effective length of query: 388 Effective length of database: 300 Effective search space: 116400 Effective search space used: 116400 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: 49 (23.5 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