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 3606890 Dshi_0320 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__Dino:3606890 Length = 432 Score = 302 bits (773), Expect = 1e-86 Identities = 178/436 (40%), Positives = 236/436 (54%), Gaps = 65/436 (14%) Query: 4 ADKPFVRTSILAAEPPPPGERGAVAWIRRNLLATPKDVILTILALALIAWAVPHLVNWLF 63 A FVRT + PPP E G V W+R NL + ILT+L A I W L+ W+F Sbjct: 6 ASAAFVRTEEIPPSPPPVSEVGIVNWLRSNLFYSIPSSILTLLTAAFIYWLSSILMPWMF 65 Query: 64 IQAVWSGPDRTFCATTLQGGIQPDGWSGACWAFISAKYDQFIFGRYPLGERWRPAIVGIL 123 VW C L G I G C+A I+ ++ Q IFG YP E WR + + Sbjct: 66 -NGVWDANSIRDCREILDGAI------GGCFAVIAERWPQLIFGNYPNEEYWRAVLAFVG 118 Query: 124 FILLLVPMLIPSAPRKGLNAILLF------------------------------------ 147 + L P+L PRK L LF Sbjct: 119 LFVALAPVLFFKLPRKMLWFTGLFPFIAYWLIWGGSAWVSVMALVGVVVGYVAFKALEER 178 Query: 148 --------AVLPVIAFWLLHG-----------GFGLEVVETPLWGGLMVTLVLSFVGIAV 188 A+ + FW+ L VE+ GG M+ +L GIA+ Sbjct: 179 SFFGAIVAALFATLLFWIFISPLAVNALSSVVALSLPQVESRFIGGFMINFILGTSGIAL 238 Query: 189 SLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVMLPLFLPTGWNVDKLL 248 SLP+GI LALGR+S +P+I+ +CV FIE IRGVPLIT+LF+ASVML FLP G + D +L Sbjct: 239 SLPLGIALALGRQSNLPIIKGVCVVFIEFIRGVPLITLLFVASVMLAYFLPPGTSFDLVL 298 Query: 249 RALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTRLIIMPQAIKLVIPSI 308 R +I +++F SAY+AE IRGGL A+P+GQ+E DSLGL YWQ RLII+PQA+K+ IPSI Sbjct: 299 RVIIMITLFASAYIAEAIRGGLAALPRGQYEAGDSLGLDYWQSMRLIILPQALKISIPSI 358 Query: 309 VNTFIGTFKDTSLVTIIGMFDLLGIVK-LNFSDANWASAVTPITGLIFAGFIFWLFCFGM 367 VN IG FKDT+LV+II MFD+LG+++ S W + G FAG +F++FC+G+ Sbjct: 359 VNIAIGLFKDTTLVSIISMFDMLGMIQGPILSSTEWFGVYWELLG--FAGVLFFVFCYGI 416 Query: 368 SRYSGFMERHLDTGHK 383 S+YS ++ER L T H+ Sbjct: 417 SQYSQWLERQLATEHR 432 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: 564 Number of extensions: 40 Number of successful extensions: 7 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: 432 Length adjustment: 31 Effective length of query: 353 Effective length of database: 401 Effective search space: 141553 Effective search space used: 141553 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: 50 (23.9 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