Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate Dsui_0636 Dsui_0636 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__PS:Dsui_0636 Length = 245 Score = 97.1 bits (240), Expect = 5e-25 Identities = 73/236 (30%), Positives = 119/236 (50%), Gaps = 22/236 (9%) Query: 156 WHWLGSLYL----SKQGIYLPWPQTPGWLVVILAIA---LVLFVSWLAQRQRSPRDWRWL 208 W+W S++L S + YL W T V L+++ + L V + R+ + RWL Sbjct: 5 WNW--SVFLTPVPSGETTYLGWLFTGLQWTVALSLSAWVIALVVGSIVGVLRTVPN-RWL 61 Query: 209 YGAIAVVT-----VLMLLTQLSW----PQQLQPG---QIRGGLRLSLEFTALLLGLVAYT 256 G AV V +L+ SW P+ L P + L +F A +L L +T Sbjct: 62 SGFAAVYVECFRNVPLLVQLFSWYFVLPELLPPALGNAYKQSDPLLQQFLAAMLCLGLFT 121 Query: 257 GAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIVPSLNSQYVGFAKN 316 A + E +R GI S+P GQ A A+G T +Q +++P A R+IVP L S+++ KN Sbjct: 122 AARVAEQVRAGIESLPRGQRNAGLAMGFTLAQVYRHVLLPMAFRIIVPPLTSEFLNIFKN 181 Query: 317 SSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISAGMNGLQQRLQ 372 S++A +G +L AQ ++ T +P E F+ + L Y+ IN + M L+++++ Sbjct: 182 SAVATTIGLIELSRQAQQLVDYTAQPYEAFIAVTLLYVCINVTVMFLMRRLEEKVR 237 Score = 42.4 bits (98), Expect = 1e-08 Identities = 25/76 (32%), Positives = 37/76 (48%) Query: 77 SYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLL 136 +Y L GL ++ + ++ V+G++ GV N L + YV RN PLL+ Sbjct: 20 TYLGWLFTGLQWTVALSLSAWVIALVVGSIVGVLRTVPNRWLSGFAAVYVECFRNVPLLV 79 Query: 137 QLIVWYFPILLSLPAA 152 QL WYF + LP A Sbjct: 80 QLFSWYFVLPELLPPA 95 Lambda K H 0.326 0.140 0.445 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: 252 Number of extensions: 18 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: 377 Length of database: 245 Length adjustment: 27 Effective length of query: 350 Effective length of database: 218 Effective search space: 76300 Effective search space used: 76300 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 (21.7 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