Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate Ac3H11_1695 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1695 Length = 309 Score = 256 bits (655), Expect = 4e-73 Identities = 141/307 (45%), Positives = 199/307 (64%), Gaps = 18/307 (5%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAF-----VALITFL 55 M+ LQQ+INGL LG++Y LIA+GYTMVYGII +INFAHGE+ MIGA + ++ Sbjct: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 Query: 56 AIGSLGITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQ 115 G+ G WV LL+ + + + A + +E++AYRPLRSSPRLAPLI+AIGMSI LQ Sbjct: 61 MPGAPG--WV--ILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQ 116 Query: 116 NYVQILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGR 175 I+ KP +LP + + GA ++ ++ + +T + L+ T+LGR Sbjct: 117 TLAMIIWKPNYKPYPTMLPSSPFEIGGAF-ITPTQILILGVTAVALASLVYLVNHTNLGR 175 Query: 176 AQRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKA 235 A RA ++ ++A L+GV D VIS TF++GA LAA+AG+M YG +GFL G+KA Sbjct: 176 AMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKA 235 Query: 236 FTAAVLGGIGSLPGAMLGGVVIGLIEAFWSGY--------MGSEWKDVATFTILVLVLIF 287 FTAAV GGIG+L GA++GG+++GLIEA SGY +GS + D+ F +L+++L Sbjct: 236 FTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTL 295 Query: 288 RPTGLLG 294 RP+GLLG Sbjct: 296 RPSGLLG 302 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: 398 Number of extensions: 19 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: 309 Length adjustment: 27 Effective length of query: 274 Effective length of database: 282 Effective search space: 77268 Effective search space used: 77268 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