Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate AO356_11625 AO356_11625 GABA permease
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_11625 Length = 464 Score = 311 bits (797), Expect = 3e-89 Identities = 163/449 (36%), Positives = 257/449 (57%), Gaps = 3/449 (0%) Query: 18 DLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGEL 77 +L +GLK RH+ M++I G IG GLF+G+G AIA AGP ++L+YA G + +MR LGE+ Sbjct: 9 NLAQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGALVVLVMRMLGEM 68 Query: 78 LLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWI 137 + P +GSF+TYA+ +G +AGF GW YW+ WV+ E A A +H WFP+V W+ Sbjct: 69 AVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPNVAIWV 128 Query: 138 PALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFS 197 L +L + N +V +GE EFWFAL+KVV I+ I +GL I FGV P + S Sbjct: 129 FTLVITLLLTVTNLFSVKNYGEFEFWFALVKVVAIIGFIGLGLMAI-FGVLPTSQVSGVS 187 Query: 198 NLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILI 257 +L+ GF+P G V+ + MF++ G E++ + A E++NP + + ATN V+WRI + Sbjct: 188 HLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNSVIWRIGL 247 Query: 258 FYVGALIIMMALVPWNE-LKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIFS 316 FY+ ++ I++ALVPWN+ L V + V ER+G+P A IV++VV+ A S NS +++ Sbjct: 248 FYLVSIFIVVALVPWNDPLLASVGSYQTVLERMGIPNAKLIVDIVVLVAVTSCLNSALYT 307 Query: 317 TGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTSIS 376 RM+++L + G AP R + P A+ S + V NY+ P VF ++ + S Sbjct: 308 ASRMMFSLGKRGDAPAVSQRTNKSGTPHWAVMLSTGAAFLAVFANYVAPAAVFEFLLASS 367 Query: 377 LVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLDPG 436 +L + +I ++ L RK A R + +AF M P + V+ F++ ++ Sbjct: 368 GAIALLVYLVIAVSQLRMRKQRMA-RGEKIAFSMWLFPGLTYAVIVFIVGALTIMLFQEA 426 Query: 437 TRVALYVAPVWFALLGIGYRFTKSRALLE 465 RV + + L+ I + R +++ Sbjct: 427 HRVEILATGLLSVLVVISGVLIQRRRIVK 455 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: 709 Number of extensions: 48 Number of successful extensions: 5 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: 464 Length adjustment: 33 Effective length of query: 439 Effective length of database: 431 Effective search space: 189209 Effective search space used: 189209 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