Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate 8501894 DvMF_2609 inner-membrane translocator (RefSeq)
Query= uniprot:A0A159ZYE0 (418 letters) >FitnessBrowser__Miya:8501894 Length = 415 Score = 333 bits (853), Expect = 7e-96 Identities = 176/313 (56%), Positives = 222/313 (70%), Gaps = 19/313 (6%) Query: 95 VLALIVGALVWPFFGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYS 154 ++ L+ LV P+ S +I L+YVMLGLGLNIVVGL+G L LGYV FYAVGAYS Sbjct: 94 LVVLLSAFLVLPWVVSTYQTNIMISALLYVMLGLGLNIVVGLSGQLVLGYVAFYAVGAYS 153 Query: 155 YALLSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNL 214 YA+L+ FGL FW LPI G MAA FG LLGFPVLRLRGDYLAIVTLGFGEIIRL L N Sbjct: 154 YAILNSNFGLGFWSVLPIGGAMAALFGILLGFPVLRLRGDYLAIVTLGFGEIIRLVLENW 213 Query: 215 TDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLAL 274 + + GP+GI+NIE+P GL G++ + + ++Y + L + Sbjct: 214 SSFSQGPSGIANIERP-------------GL------LGMQLSVSDATTYIYYLILAAVI 254 Query: 275 AALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAAR 334 + + RL IGRAW+ALREDEIAC+A+G++ T KL+AF LGA +AGFAG FAA+ Sbjct: 255 VTILAVTRLKNSRIGRAWQALREDEIACQAMGIDITTTKLTAFALGACWAGFAGVIFAAK 314 Query: 335 QGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEMMREFSEYRMLMFGAL 394 + P SFTF+ESA++LA+VVLGGMGS +GV + A+V+ILLPE +R FSEYRML+FGA Sbjct: 315 TTFINPASFTFLESAMVLAMVVLGGMGSVIGVSVGALVLILLPEYLRAFSEYRMLIFGAT 374 Query: 395 MVLMMIWRPQGLL 407 MVLMM++RPQGL+ Sbjct: 375 MVLMMVFRPQGLV 387 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: 578 Number of extensions: 25 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: 418 Length of database: 415 Length adjustment: 31 Effective length of query: 387 Effective length of database: 384 Effective search space: 148608 Effective search space used: 148608 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