Align L-alanine and D-alanine permease (characterized)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily
Query= reanno::pseudo5_N2C3_1:AO356_17670 (473 letters) >FitnessBrowser__Dyella79:N515DRAFT_2630 Length = 454 Score = 711 bits (1834), Expect = 0.0 Identities = 338/442 (76%), Positives = 394/442 (89%) Query: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 L+R L ERHIRLMALG+ IGVGLFLGSA AI +AGPAI+LSY++GG+AI +IMRALGEMA Sbjct: 7 LQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPAILLSYLLGGVAIFIIMRALGEMA 66 Query: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137 V NPVAGSFSRYAQDYLGPL G+LTGWNYWF+WL+TC+AEITAV VYMG+WFPDVP+WIW Sbjct: 67 VQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDVPQWIW 126 Query: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197 ALAALV+MG++NL AVKA+GEFEFWFA+IK+VTI+ M++GG +I FG GN GV GISN Sbjct: 127 ALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQGVPTGISN 186 Query: 198 LWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLF 257 LW HGGFMPNG G+LM+LQMVMFAYLGVEMIGLTAGEA NP+K+IP+AI SVFWRIL+F Sbjct: 187 LWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAINSVFWRILIF 246 Query: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317 YVGALFVI+SIYPWNE+GT GSPFVMTFERLGIK+AAGIINFVV+TAALSSCNGGI+STG Sbjct: 247 YVGALFVIMSIYPWNELGTHGSPFVMTFERLGIKSAAGIINFVVLTAALSSCNGGIYSTG 306 Query: 318 RMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIATF 377 RML++LAQ GQAP FA TS +G+P RA+L+S+ ALL GVLLNYLVP KVFVWVTS ATF Sbjct: 307 RMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYLVPAKVFVWVTSAATF 366 Query: 378 GAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFPDTR 437 GAIWTW ++L+ Q+K+R+ LS ++R+ L +RM +P +SYLALAFLVLVVGLM YFPDTR Sbjct: 367 GAIWTWGIVLITQMKYRRGLSEAQRSQLVFRMPFFPYASYLALAFLVLVVGLMGYFPDTR 426 Query: 438 VALYVGPAFLVLLTVLFYTFKL 459 VAL VGP +LVLLTVL+Y F L Sbjct: 427 VALIVGPLWLVLLTVLYYVFGL 448 Lambda K H 0.328 0.142 0.444 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: 821 Number of extensions: 34 Number of successful extensions: 1 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: 473 Length of database: 454 Length adjustment: 33 Effective length of query: 440 Effective length of database: 421 Effective search space: 185240 Effective search space used: 185240 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: 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