Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate 3606889 Dshi_0319 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_09910 (229 letters) >FitnessBrowser__Dino:3606889 Length = 411 Score = 66.6 bits (161), Expect = 7e-16 Identities = 38/107 (35%), Positives = 64/107 (59%), Gaps = 1/107 (0%) Query: 102 MTLHTAAYIAEILRGAIQAIPKGEIEAARALGMSRPKALFYIMLPRAARIGLPAYSNEVI 161 + L+T A+IAE +R I A+ KG+ EAA ALGM + + I+LP+A R+ +P ++ + Sbjct: 286 LALYTGAFIAENVRAGILAVSKGQTEAAAALGMRPNRIMSLIILPQALRVIIPPVISQYL 345 Query: 162 LMLKASALASTVTLLELTG-MARTIIARTYLPVEIFFAAGMFYLLMS 207 + K S+LA+ + ++LTG + + +T E +FYLL+S Sbjct: 346 NLTKNSSLAAAIGYMDLTGTLGGVTLNQTGRSFECVLLLMLFYLLIS 392 Score = 32.3 bits (72), Expect = 1e-05 Identities = 22/100 (22%), Positives = 39/100 (39%), Gaps = 19/100 (19%) Query: 16 GATLTLELVAIAVIAGLLLAIPLGIARSSRLWQVRALPYAYIFFFRGTPLLVQLFLVYYG 75 G TL + + I + + G+ R S+ W V + Y+ FR P+L+ + ++ Sbjct: 97 GLLNTLLVAFLGCITATIFGVLAGVLRLSKNWLVAKVMSVYVEIFRNIPVLIWIVIISAV 156 Query: 76 LAQF----------DAVRSSALWP---------YLRDPFW 96 ++Q DA + LW Y+ P W Sbjct: 157 MSQALPQPRAFRGEDATATMVLWDSVAFTNRGVYIPAPVW 196 Lambda K H 0.331 0.141 0.434 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: 208 Number of extensions: 8 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 229 Length of database: 411 Length adjustment: 27 Effective length of query: 202 Effective length of database: 384 Effective search space: 77568 Effective search space used: 77568 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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