Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate 206676 DVU1237 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= uniprot:Q31RN9 (396 letters) >MicrobesOnline__882:206676 Length = 256 Score = 125 bits (313), Expect = 2e-33 Identities = 69/203 (33%), Positives = 118/203 (58%), Gaps = 7/203 (3%) Query: 190 GLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVTILFFGQVM 249 G+L+T + S++CS+P+G++ LGR S I ++ TY+E+ RG+PL+ LF+ Sbjct: 55 GILVTFQVTVFSIICSIPIGLITGLGRLSRNRGINLVASTYVEVVRGIPLLVQLFY---- 110 Query: 250 VPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALGLNLFQTYR 309 + L ++ +L AI+ L++ AY+ E R G++AIP+GQ EAA +LG N +T Sbjct: 111 IYYALGRFLKVPDMLAAIIALSVCYGAYMGEVFRAGIEAIPKGQTEAARSLGFNRVETMF 170 Query: 310 FIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYLGRYAEVYLF 369 +VLPQA R +P + F+ +L+DT+L+SI+ + ++L R + +Y E Y Sbjct: 171 LVVLPQAWRTILPPVGNEFIAMLKDTSLVSIIAVADILRRGREFASESF---QYFETYTM 227 Query: 370 LGVLYWLCCYGLAQLSRRLEQRL 392 + ++Y L L++ +E RL Sbjct: 228 IALVYLLITLLLSKGVSIMEARL 250 Lambda K H 0.329 0.142 0.471 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: 232 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: 396 Length of database: 256 Length adjustment: 27 Effective length of query: 369 Effective length of database: 229 Effective search space: 84501 Effective search space used: 84501 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: 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