Align D-alanine and L-alanine transporter (characterized)
to candidate Ga0059261_1053 Ga0059261_1053 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= reanno::pseudo3_N2E3:AO353_16120 (472 letters) >FitnessBrowser__Korea:Ga0059261_1053 Length = 512 Score = 98.6 bits (244), Expect = 4e-25 Identities = 110/488 (22%), Positives = 204/488 (41%), Gaps = 66/488 (13%) Query: 12 TAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMR 71 TA+ L R LG + ++ +GA IG G+F+ +A+A + AGP +MLS++I G+ V Sbjct: 15 TAEKKSLHRSLGAFQLTMLGIGAVIGTGIFVLTAEAAQKAGPGMMLSFVIAGVVCAVAAL 74 Query: 72 ALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNY--------------WFLWLVTCVAE 117 EMA PV+GS Y+ +G L ++ GW W ++V + Sbjct: 75 CYAEMAAMVPVSGSAYTYSYAVMGELIAWMVGWALILEYAVAAGAVSVGWSGYVVGLIEN 134 Query: 118 ITAVAVYMGIWFPEVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVVG 177 A+ + + I L A++ G + + V E F +++ +V + A+ + Sbjct: 135 AFALDIPDALVRGPYDGGIINLPAMLIAGLVTWLLVIGTKESAFVNSVLVLVKVSALSLF 194 Query: 178 GVGVIAFGFGNDGVALGISNLWSHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAK 237 + +A+ + N+ + F P G GV + + FAY+G + + A E K Sbjct: 195 II-----------LAIPVMNMQNFEPFSPLGFAGVSAAAASIFFAYVGFDAVSTAAEETK 243 Query: 238 NPQKTIP-NAIGSVFWRILLFYVGALFVILSIYPWNEIGTQGS---PFVMTFERLGIKTA 293 NPQ+ +P IGS+ + + + A VI S+ +G G+ P + ++TA Sbjct: 244 NPQRNMPIGLIGSLAICTIFYLLVAAGVIGSVGAQPILGPDGAALPPGSTELTKACVETA 303 Query: 294 AG------------------------IINFVVITAAL---SSCNGGIFSTGRMLYSLAQN 326 A I N + + A L S +F R+ + ++++ Sbjct: 304 AATGKEAVVCSKEALAWTLREIGWPQIGNLIGLAAGLALPSVILMMMFGQTRIFFVMSRD 363 Query: 327 GQAPAGFAKTSNGVPRRALLLSIGALLLGVLLNYLVPEKVFVWVTAIATFGAIWTWVMIL 386 G PA F+K ++ + + + + + K + I+ G ++ + + Sbjct: 364 GLLPAVFSKVHPKFHTPHVITILTGVFVALFAAFFPVGK----LADISNSGTLFAFAAVS 419 Query: 387 LAQLKFRKGLSPAERAALKYRMWLYPVSSYLALAFLVMVVGLMAYFPDTRVALYVGPAFL 446 +A L R+ +R + + + L A+L +G DT++ ++VG A L Sbjct: 420 IAVLVLRRTDPDRKRPFRTPLIIITAPIAILGCAYLFYSLG-----HDTKM-MFVGWAAL 473 Query: 447 VLLTVLFY 454 LL Y Sbjct: 474 GLLVYFGY 481 Lambda K H 0.328 0.142 0.446 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: 569 Number of extensions: 30 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: 472 Length of database: 512 Length adjustment: 34 Effective length of query: 438 Effective length of database: 478 Effective search space: 209364 Effective search space used: 209364 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: 52 (24.6 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