Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate 3608831 Dshi_2223 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_03050 (229 letters) >FitnessBrowser__Dino:3608831 Length = 295 Score = 100 bits (248), Expect = 4e-26 Identities = 71/253 (28%), Positives = 116/253 (45%), Gaps = 44/253 (17%) Query: 12 GAWLTLQLALSSMALAIVL----GLIGVALRLSPIRWLARLGDLYSTVIRGIPDLVLILL 67 G++ T+ L L A A + G I +++P+RWL G Y++++RGIPD+ L Sbjct: 31 GSFGTVMLLLVVTAPAALFLGFGGAIAARSQIAPLRWL---GKGYTSMVRGIPDIAFFLF 87 Query: 68 IFYG-----------------------GQDLL---NRVAPLLGYDDYI-DLNPLVAGIGT 100 + G D + PL ++ + + Sbjct: 88 VPIALDQGLEYLRHHWKCPDWTQAVRQGNDFVVCAEAKLPLSTSPQWVHETYGFTLAVIA 147 Query: 101 LGFIFGAYLSETFRGAFMAIPKGQAEAGAAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWL 160 +FGA+ + GA A+P+ Q E AYGM+ Q F+R+LVPQM A+PG +N W Sbjct: 148 FAVVFGAFAANVLYGAMTAVPRAQIETAEAYGMTRRQAFWRILVPQMWVYALPGLSNLWQ 207 Query: 161 VLTKATALISVVGLQDMMFKAKQAADATREPFT----------FFLAVAAMYLVITSVSL 210 +L KAT L+ ++G++D+++ A++ F+ +FL + YL +TSVS Sbjct: 208 ILVKATPLLFLLGIEDIVYWARELGGVQSARFSDYPHGDWRLWYFLGLLVFYLALTSVSE 267 Query: 211 LALRHLEKRYSVG 223 L +R S G Sbjct: 268 RIFARLMQRLSHG 280 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: 196 Number of extensions: 13 Number of successful extensions: 4 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: 295 Length adjustment: 24 Effective length of query: 205 Effective length of database: 271 Effective search space: 55555 Effective search space used: 55555 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