Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF1277 Psest_1310 ABC-type branched-chain amino acid transport system, permease component
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__psRCH2:GFF1277 Length = 418 Score = 356 bits (913), Expect = e-103 Identities = 199/339 (58%), Positives = 239/339 (70%), Gaps = 19/339 (5%) Query: 116 LLYPMVVVAIKGP-QGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGA 174 ++ +V+VA+ P GS VD ILIYVML GLNIVVGLAGLLDLGYV FYAVGA Sbjct: 94 IILALVLVALVWPFYGSRGAVD-IATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGA 152 Query: 175 YSYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLI 234 Y+YALLS Y+G+ FW LP++G AAL+G +LGFPVLRLRGDYLAIVTL FGEIIR++L Sbjct: 153 YTYALLSHYYGVGFWTALPIAGAMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLR 212 Query: 235 NWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYK----IFLFYLILAL 290 N T VT G GIS I K TLFG+ FD A + FH AY IFL+ + L L Sbjct: 213 NMTSVTGGPNGISGIDKPTLFGLSFDRRAAEGMQTFHEYFGVAYNSVNKVIFLYLIALLL 272 Query: 291 CMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFA 350 +LT +V RL RMPIGRAWEALREDEIACR+LG+N KL+AF GA FAGFAGSFFA Sbjct: 273 VLLTLFVINRLLRMPIGRAWEALREDEIACRALGMNPTVIKLSAFTLGATFAGFAGSFFA 332 Query: 351 ARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGP 410 ARQG VSPESF F+ESA+ILAIVVLGGMGS G+ +AAIVM+ EL+RE S Sbjct: 333 ARQGLVSPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPELMREFS-------- 384 Query: 411 DFTPELYRMLIFGLAMVVVMLFKPRGFVGSREPTAFLRE 449 YRML+FG MV++M+++P+G + + P L++ Sbjct: 385 -----EYRMLMFGALMVLMMIWRPQGLLPMQRPHLELKQ 418 Lambda K H 0.330 0.145 0.432 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: 640 Number of extensions: 37 Number of successful extensions: 3 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: 463 Length of database: 418 Length adjustment: 32 Effective length of query: 431 Effective length of database: 386 Effective search space: 166366 Effective search space used: 166366 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: 51 (24.3 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