Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate 3608832 Dshi_2224 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_03050 (229 letters) >FitnessBrowser__Dino:3608832 Length = 268 Score = 74.7 bits (182), Expect = 2e-18 Identities = 63/208 (30%), Positives = 96/208 (46%), Gaps = 21/208 (10%) Query: 25 ALAIVLGLI---GVALRLSPIRWLARL-GDLYSTVIRGIPDLVLILLIFYGGQDLLNRVA 80 A A++ G VAL + R + R+ D + V RG P + L ++ L V+ Sbjct: 48 AFALLFGFFLATAVALGKASDRAVLRVPADWFIFVFRGSPLFIQFFLAYFLFIQL-KAVS 106 Query: 81 PLLGYDDYIDLNPLVAGIGTLGFIF---GAYLSETFRGAFMAIPKGQAEAGAAYGMSSFQ 137 P +D + A G L +F AY E F GA ++PKG EA AYG++ + Sbjct: 107 P--AFDPFTS-----AWAGALVVLFLNTSAYAGEIFYGALRSVPKGDLEAADAYGLAGWT 159 Query: 138 VFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQ------DMMFKAKQAADATREP 191 F RV P M+RLA P +TN + L AT L+ G D ++ A+ AD T P Sbjct: 160 KFRRVTWPTMLRLAWPSYTNEAIFLFHATTLVFFAGFPAFQQRGDALYYAQYFADKTFNP 219 Query: 192 FTFFLAVAAMYLVITSVSLLALRHLEKR 219 F + VA ++++T + + +R Sbjct: 220 FIPYPIVAFYFILLTLAVIFVFSLINRR 247 Lambda K H 0.329 0.144 0.421 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: 183 Number of extensions: 11 Number of successful extensions: 1 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: 229 Length of database: 268 Length adjustment: 24 Effective length of query: 205 Effective length of database: 244 Effective search space: 50020 Effective search space used: 50020 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: 46 (22.3 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