Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate AZOBR_RS18065 AZOBR_RS18065 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >FitnessBrowser__azobra:AZOBR_RS18065 Length = 219 Score = 110 bits (275), Expect = 3e-29 Identities = 66/207 (31%), Positives = 119/207 (57%), Gaps = 12/207 (5%) Query: 161 TLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLF 220 T+V++ V +G LG+ L R A R+ ++E ++G PL+ LF++ L LF Sbjct: 20 TVVLSLVSFIGGGLLGMALLYLRIGKARAGRMFVQGYVELFQGTPLLMQLFLAFFGLGLF 79 Query: 221 LPEGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVIL 280 G++ L A + ++L+ +A++ E+ RG ++++ +GQ+EA+A++G+GY + M VIL Sbjct: 80 ---GIDVPAWLAAGLALVLWTAAFLVEIWRGCVESVARGQWEASASLGMGYVQQMRYVIL 136 Query: 281 PQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNS---VKQAAADPKWLGMATEGYVFA 337 PQA+++ +P V + + K T+L IIG +L + V A +P + Y Sbjct: 137 PQAVRVAVPPTVGFSVQVVKGTALTSIIGFVELSKAGTVVTNATFEPFTV------YGLV 190 Query: 338 ALVFWIFCFGMSRYSMHLERKLDTGHK 364 AL+++ C+ +S+ S LERKL+ H+ Sbjct: 191 ALIYFALCWPLSKSSQILERKLNVAHR 217 Lambda K H 0.330 0.144 0.469 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: 263 Number of extensions: 9 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: 365 Length of database: 219 Length adjustment: 26 Effective length of query: 339 Effective length of database: 193 Effective search space: 65427 Effective search space used: 65427 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 (21.9 bits) S2: 47 (22.7 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