Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate 3606951 Dshi_0379 inner-membrane translocator (RefSeq)
Query= uniprot:A0A159ZYE0 (418 letters) >FitnessBrowser__Dino:3606951 Length = 358 Score = 141 bits (356), Expect = 3e-38 Identities = 101/331 (30%), Positives = 167/331 (50%), Gaps = 37/331 (11%) Query: 93 WIVLALIVGALVWPF-FGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVG 151 ++VLA+ VG + PF A + LI+ + +GLNI+ G G + LG GF AVG Sbjct: 30 YLVLAVAVGII--PFVINDYWASAVMVPFLIWAIAAIGLNILTGYCGQVSLGTGGFMAVG 87 Query: 152 AYS-YALLSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGE-IIRL 209 AY+ Y L++ + L+ IC+ + G++ A G L G P LR++G YLA+ TL ++ L Sbjct: 88 AYACYKLMTAFPDLNIAICVLLGGVITAAVGVLFGLPSLRIKGFYLAVATLAAQFFLVWL 147 Query: 210 FLRNLTDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVA 269 F + +G N + T FG A+ + L+ +A Sbjct: 148 FNKVPWFYNYSASGQINAPERTMFGYAITGPNADAAPKY----------------LFCLA 191 Query: 270 LLLALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGS 329 L LA ++ L R IGR+W A+R+ +IA +G+NP KL+AF + + F G AG+ Sbjct: 192 FLFVLA--WLARNLTRGTIGRSWMAIRDMDIAAEIIGVNPLKAKLTAFAVSSFFVGVAGA 249 Query: 330 -FFAARQGLV-TPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEMMREF---- 383 FF+ G V E+F +S ++L ++++GG+GS G + A ++LLP +++ Sbjct: 250 LFFSVYLGAVEVGEAFGINQSFLVLFMIIIGGLGSIFGSLAGAAFIVLLPVLLKNVMVGS 309 Query: 384 --------SEYRMLMFGALMVLMMIWRPQGL 406 + + ++ G L++ +I P GL Sbjct: 310 LGWDTAIAAHFEFVVLGGLIIFFLIVEPHGL 340 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: 463 Number of extensions: 26 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: 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