Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate PP_1059 PP_1059 Uncharacterized amino acid permease YtnA
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__Putida:PP_1059 Length = 472 Score = 511 bits (1315), Expect = e-149 Identities = 245/437 (56%), Positives = 325/437 (74%) Query: 19 LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGELL 78 L R L +RHI+++A+G IGVGLFLG+ +AI +AGP +MLSY IGG+AI IMRALGE+ Sbjct: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 Query: 79 LYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWIP 138 ++ PV+GSF+ YA++++GP AGF TGW+YWF+W+VT +AEITAVA+Y+ WFPDVP+WI Sbjct: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAIYMGIWFPDVPRWIW 137 Query: 139 ALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFSN 198 ALA L + VN VAV FGE EFWFALIK+VTI+AM++ G+ II FG G SN Sbjct: 138 ALAALGSMGAVNLVAVKAFGEFEFWFALIKIVTIIAMVLGGIGIIAFGFGNDGVAVGISN 197 Query: 199 LWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILIF 258 LW++GGFMP G GV+++LQ+VMFAY GVE+IG+TAGEA+NP+K +P A V WRIL+F Sbjct: 198 LWSNGGFMPNGVTGVLMSLQMVMFAYLGVEMIGLTAGEARNPQKTIPQAIGSVFWRILLF 257 Query: 259 YVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIFSTG 318 YVGAL +++++ PWNE+ SPFV FER+G+ AA I+N VVITAA SSCN GIFSTG Sbjct: 258 YVGALFVILSIYPWNEIGSQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317 Query: 319 RMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTSISLV 378 RMLY+LAQ GQAP AF R S VP A+ S + +GVL NY+VPE+VFVWVTSI+ Sbjct: 318 RMLYSLAQNGQAPAAFARTSKNGVPRNALLLSIGALLLGVLANYLVPEKVFVWVTSIATF 377 Query: 379 GSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLDPGTR 438 G++WTW +I++A L +R + KA+ +RM P +++L +AF++ V L++ TR Sbjct: 378 GAIWTWVMILLAQLKFRAGLTTAERKALKYRMWLWPLSSYLALAFLVLVVGLMAYFEDTR 437 Query: 439 VALYVAPVWFALLGIGY 455 VALY+ P + LL + Y Sbjct: 438 VALYIGPAFLVLLTVLY 454 Lambda K H 0.328 0.142 0.445 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: 872 Number of extensions: 51 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: 472 Length of database: 472 Length adjustment: 33 Effective length of query: 439 Effective length of database: 439 Effective search space: 192721 Effective search space used: 192721 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