Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate BWI76_RS07280 BWI76_RS07280 branched-chain amino acid ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__Koxy:BWI76_RS07280 Length = 316 Score = 250 bits (639), Expect = 3e-71 Identities = 137/309 (44%), Positives = 200/309 (64%), Gaps = 15/309 (4%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60 M+ +QQ+ING+ LG+IY LIA+GYTMVYGI+ +INFAHG+I M+GA L A+ + Sbjct: 1 MDTLIQQIINGVMLGSIYALIALGYTMVYGILRIINFAHGDILMVGALTTLSGMHALNAH 60 Query: 61 GITWVPLALL-VMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQ 119 T PLA L + L+ +M A+ VER AYR LR++PRLAPLIS IG+S+ LQ Sbjct: 61 FPTLPPLAQLGLALLLAMTVCALLAMAVERFAYRRLRNAPRLAPLISGIGVSVLLQTVAM 120 Query: 120 ILQGARSKPLQPILPGN-LTLMDGAVS-----VSYVRLATIVITIALMYGFTQLITRTSL 173 I+ ILP + + + G+ + ++ + T+ + + +M G L+ T L Sbjct: 121 IVWSRNPLMFPQILPMDPIAVTHGSAAHPPALITVTGIVTVALALTVMLGLWLLVEYTRL 180 Query: 174 GRAQRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGV 233 GR RA ++ ++A L+GVN + +I+LTF +G AA+AG+M+ YG F +GFL G+ Sbjct: 181 GRGMRAVAENPRIATLMGVNPNAIIALTFAIGGVFAALAGVMMASNYGSAGFSMGFLPGI 240 Query: 234 KAFTAAVLGGIGSLPGAMLGGVVIGLIEAFWSGYM--------GSEWKDVATFTILVLVL 285 KAFTAAVLGGIG++ GAM+GG+++GLIE+ +GY+ GS ++D+ F +L+LVL Sbjct: 241 KAFTAAVLGGIGNIRGAMIGGLLLGLIESLGAGYLGDLTHGVFGSNYQDIFAFMVLILVL 300 Query: 286 IFRPTGLLG 294 +FRP GLLG Sbjct: 301 VFRPAGLLG 309 Lambda K H 0.329 0.144 0.425 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: 351 Number of extensions: 14 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: 301 Length of database: 316 Length adjustment: 27 Effective length of query: 274 Effective length of database: 289 Effective search space: 79186 Effective search space used: 79186 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: 48 (23.1 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