Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate 209487 DVU0548 high-affinity branched-chain amino acid ABC transporter, permease protein
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >MicrobesOnline__882:209487 Length = 302 Score = 311 bits (796), Expect = 2e-89 Identities = 158/303 (52%), Positives = 226/303 (74%), Gaps = 7/303 (2%) Query: 2 EYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLG 61 +YF + L GL+ G+IY LIA+GYTMVYGII +INFAHGE+YMIGAF ALI G LG Sbjct: 4 QYFCELLFGGLTRGSIYALIALGYTMVYGIIELINFAHGEVYMIGAFTALIV---AGVLG 60 Query: 62 ITWVPLA--LLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQ 119 I P A L++ + ++++ A YG+T+E++AY+PLR +PRL+PLISAIGMSIFLQNYV Sbjct: 61 IYGFPEAGILIIAAIVAVIYCAAYGFTLEKVAYKPLRDAPRLSPLISAIGMSIFLQNYVI 120 Query: 120 ILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIAL-MYGFTQLITRTSLGRAQR 178 + Q + P ++P +L +++ ++ I++T A+ M G T I T +G+A R Sbjct: 121 LAQTSDFVPFPRLVP-DLAILEPIAHITGTSDVLIIVTSAITMVGLTLFIKYTRMGKAMR 179 Query: 179 ACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTA 238 A Q++KMA LLG++ DRVISLTF++G++LAA+ G+++ G ++F IGF+AG+KAFTA Sbjct: 180 ATAQNRKMAMLLGIDADRVISLTFIIGSSLAAIGGVLIASHIGQVNFAIGFIAGIKAFTA 239 Query: 239 AVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEI 298 AVLGGIGS+PGAM GG+V+GL E+F +GY+ S+++D F +LVL+LIFRP+G+LG+P+ Sbjct: 240 AVLGGIGSIPGAMAGGLVLGLCESFATGYVSSDYEDALAFALLVLILIFRPSGILGKPKT 299 Query: 299 EKV 301 +KV Sbjct: 300 QKV 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: 389 Number of extensions: 18 Number of successful extensions: 5 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: 302 Length adjustment: 27 Effective length of query: 274 Effective length of database: 275 Effective search space: 75350 Effective search space used: 75350 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