Align L-Arginine ABC transporter, permease protein AotQ (characterized)
to candidate 8501972 DvMF_2686 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5661 (229 letters) >FitnessBrowser__Miya:8501972 Length = 316 Score = 105 bits (263), Expect = 8e-28 Identities = 68/211 (32%), Positives = 111/211 (52%), Gaps = 14/211 (6%) Query: 9 ILDGAWLTLELALSSMALAIVLGLIGVALRLSPVRWLAWLGDLYATVIRGIPDLVLILLI 68 +LDG +T+++ +S+ LA++ GL+ LR S R L Y +R P L+ + ++ Sbjct: 114 LLDGLGVTVQVVAASLGLALLAGLLAALLRQSGSRVGRALAVAYVETVRNTPLLIQLFVV 173 Query: 69 FYGGQDLLNRVAPMLGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEAG 128 ++ +AP+LG L AAG+ L GAY++E R +++P GQ EA Sbjct: 174 YFV-------LAPVLG------LGRFAAGVLALSLFEGAYIAEILRAGILSVPTGQWEAS 220 Query: 129 MAYGMNGFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADAT 188 + GM+ + V++PQ R A+P T + L K ++L+S + L D+ +A+ A T Sbjct: 221 RSLGMDVPGTYMEVVLPQAARTALPPLTGQLVSLVKDSSLVSTIALHDLAMQAQAVAADT 280 Query: 189 REPFTFFLAVAAMYLVITSVSLLALRHLEKR 219 F + VA MYL +T +SL AL L +R Sbjct: 281 FLVFEVWFLVAGMYLALT-LSLSALAQLLER 310 Lambda K H 0.329 0.144 0.429 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: 191 Number of extensions: 13 Number of successful extensions: 2 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: 316 Length adjustment: 25 Effective length of query: 204 Effective length of database: 291 Effective search space: 59364 Effective search space used: 59364 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: 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