Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate BWI76_RS19235 BWI76_RS19235 polar amino acid ABC transporter inner membrane subunit
Query= reanno::pseudo3_N2E3:AO353_03050 (229 letters) >FitnessBrowser__Koxy:BWI76_RS19235 Length = 230 Score = 204 bits (518), Expect = 2e-57 Identities = 101/222 (45%), Positives = 155/222 (69%), Gaps = 1/222 (0%) Query: 1 MLKGYGAVILDGAWLTLQLALSSMALAIVLGLIGVALRLSPIRWLARLGDLYSTVIRGIP 60 M+ Y ++L GA L+L + LSS+ +A++LGLI ++L WL Y+T++RGIP Sbjct: 1 MVADYLPLLLRGAALSLCVMLSSLLVALLLGLINSLIKLFGPPWLRLFSTAYTTLVRGIP 60 Query: 61 DLVLILLIFYGGQDLLNRVAPLLGYDDYIDLNPLVAGIGTLGFIFGAYLSETFRGAFMAI 120 +LV++LL+F+GG+ L+N + L+G + N ++G+ +GF+FGAY +ETFRGAF+ + Sbjct: 61 ELVIMLLLFFGGEMLVNLLLGLVGLGP-VRFNTFISGVLAIGFVFGAYYTETFRGAFLTV 119 Query: 121 PKGQAEAGAAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFK 180 GQ EA AYGM + VF RV++PQM+ AIPG NNWL L KA+AL+S++GL+DM++ Sbjct: 120 DSGQTEAAQAYGMRPWTVFRRVMLPQMLSFAIPGINNNWLGLMKASALVSILGLEDMVWL 179 Query: 181 AKQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSV 222 A+QA AT++PF F+ V+ +Y+VIT++S L KRY++ Sbjct: 180 AEQAGRATQKPFLFYFLVSLIYMVITALSSWLFSRLAKRYAL 221 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: 191 Number of extensions: 8 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: 230 Length adjustment: 23 Effective length of query: 206 Effective length of database: 207 Effective search space: 42642 Effective search space used: 42642 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