Align AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate 8502073 DvMF_2786 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__Miya:8502073 Length = 596 Score = 140 bits (352), Expect = 1e-37 Identities = 78/206 (37%), Positives = 122/206 (59%), Gaps = 6/206 (2%) Query: 173 GGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASV 232 GGL +L+++ + I+VS +G+ + +GR S V R+ C+ +IE+IRG PLI V+F Sbjct: 388 GGLAYSLLMAVIAISVSFFIGLAVGVGRSSSNRVFRIPCLLYIELIRGNPLIIVIFWVYF 447 Query: 233 MLPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKT 292 +P+ T NV A ++ FT AY+AE++R G+Q IP GQ E A S GL Y Q Sbjct: 448 FIPVMFGTTLNV--FWSATWALTAFTGAYIAEIVRTGIQNIPAGQVEAAYSTGLTYLQAM 505 Query: 293 RLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITG 352 R I++PQA+K +IP+IV FI FKDTSL ++G+ +L + + N + P+ Sbjct: 506 RRIVLPQALKQMIPAIVGQFIAIFKDTSLAFVLGVLELTFVAQ----GINNRLMIHPMEI 561 Query: 353 LIFAGFIFWLFCFGMSRYSGFMERHL 378 F++++ C+ MS ++ +ER L Sbjct: 562 YGTVAFLYFICCYSMSVFAARLERRL 587 Score = 105 bits (261), Expect = 4e-27 Identities = 61/163 (37%), Positives = 94/163 (57%), Gaps = 6/163 (3%) Query: 174 GLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVM 233 GL T+ +S + A++L +G +L L R S +R+ IE R PL+ LF Sbjct: 60 GLANTVRISLISSALALLLGTMLGLARLSLFRPLRVTATCVIEFFRNTPLLIQLFFWYFA 119 Query: 234 LPLFLPTG-----WNVD-KLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLG 287 P LP +++ + A IG+SI+T+++MAEVIR GLQ+IPKG E A S GL Sbjct: 120 FPAILPDNAREALFSIQFEFWCATIGLSIYTASFMAEVIRAGLQSIPKGLLEAAYSSGLS 179 Query: 288 YWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDL 330 Y+Q R II+P A + +IP + + F+ K++SL ++G+ +L Sbjct: 180 YFQVLRTIILPLAFRAIIPPLGSEFLNNMKNSSLAMVVGVAEL 222 Lambda K H 0.330 0.145 0.469 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: 615 Number of extensions: 42 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 384 Length of database: 596 Length adjustment: 34 Effective length of query: 350 Effective length of database: 562 Effective search space: 196700 Effective search space used: 196700 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: 51 (24.3 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