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 206177 DVU0751 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= TCDB::Q52814 (384 letters) >MicrobesOnline__882:206177 Length = 596 Score = 145 bits (365), Expect = 4e-39 Identities = 80/206 (38%), Positives = 126/206 (61%), Gaps = 6/206 (2%) Query: 173 GGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASV 232 GGL +L+++ + I+VS +G+++ +GR S + R+ C+ +IE+IRG PLI V+F Sbjct: 388 GGLAYSLLMAVIAISVSFFIGLVVGIGRTSDNRICRIPCLLYIELIRGNPLIIVIFWIYF 447 Query: 233 MLPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKT 292 +P+ T +NV A I +++FT AY+AE++R G+Q IP GQ E A S GL + Q Sbjct: 448 FIPVLFNTFFNV--FWSATIALTLFTGAYLAEIVRAGIQNIPAGQVEAAYSTGLTFVQTM 505 Query: 293 RLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVTPITG 352 R II+PQA+K +IP+IV FI FKDTSL ++G+ +L + + N V P+ Sbjct: 506 RRIILPQALKQMIPAIVGQFIAIFKDTSLAFVLGVLELTFVAQ----GINNRLMVYPMEI 561 Query: 353 LIFAGFIFWLFCFGMSRYSGFMERHL 378 F++++ C+ MS Y+ +ER L Sbjct: 562 YGTVAFLYFICCWSMSVYAARLERRL 587 Score = 113 bits (283), Expect = 1e-29 Identities = 81/234 (34%), Positives = 121/234 (51%), Gaps = 26/234 (11%) Query: 163 GLEVVETPLWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVP 222 GLE+++ GL VT+ +S + A++L +G +L + R S +R+ +E R P Sbjct: 54 GLEILK-----GLGVTVRISLISSALALGLGTVLGIARLSLFAPLRLTATAVVEFFRNTP 108 Query: 223 LITVLFMASVMLPLFLPTGWNVDKLLR--------ALIGVSIFTSAYMAEVIRGGLQAIP 274 L+ LF P LP N+ +LL A IG+S++TSA+MAEVIR GLQ+IP Sbjct: 109 LLVQLFFWYFAFPAILPE--NIRELLFTGNFEFWCATIGLSVYTSAFMAEVIRAGLQSIP 166 Query: 275 KGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLL--- 331 KG E A S GL Y Q R II+P A + +IP + + F+ K++SL ++G+ +L Sbjct: 167 KGLLEAAYSSGLNYVQVLRTIILPMAFRAIIPPLGSEFLNNMKNSSLAMVVGVAELTWQS 226 Query: 332 -GIVKLNFSDANWASAVTPITGLIFAGFIFWLFCFGMSRYSGFMERHLDTGHKR 384 + L F SA T + + L F ++ +G M LDT KR Sbjct: 227 QQVESLTFKGFEATSAAT-----VLYLSLSLLISFILNGVNGKM--RLDTAPKR 273 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: 664 Number of extensions: 41 Number of successful extensions: 5 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: 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