Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate Pf6N2E2_1423 Gamma-aminobutyrate permease
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1423 Length = 466 Score = 293 bits (750), Expect = 8e-84 Identities = 155/423 (36%), Positives = 249/423 (58%), Gaps = 6/423 (1%) Query: 19 LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGELL 78 L +G K RH+ M++I G IG GLF+G+G AIA AGP +ML+Y G+ + +MR LGE+ Sbjct: 13 LAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPAVMLAYLFSGLLVVLVMRMLGEMA 72 Query: 79 LYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWIP 138 + P +GSF+TYA++ +G +AGF GW YW+ WV+ E A ++ WFP + W+ Sbjct: 73 VANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVLNQWFPAIDAWLF 132 Query: 139 ALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFSN 198 A ++ +L + N +V+ +GE EFWFA+ KVV I+ I +G A++ G P + S Sbjct: 133 ASVSIVLLAVTNLFSVSKYGEFEFWFAMAKVVAIIGFISLGFAVL-MGWIPEREASGLSR 191 Query: 199 LW-THGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILI 257 L HGGF P G VV +MF++ G E + + A E+ NP + + AT V+WRI + Sbjct: 192 LMEEHGGFAPNGLSAVVGAFITIMFSFIGTEAVTIAAAESDNPAQNIAKATRSVIWRIGV 251 Query: 258 FYVGALIIMMALVPWNE-LKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIFS 316 FY+ ++ +++++VPWN+ L V + E + +P A +V++VV+ A AS NS I+ Sbjct: 252 FYLLSIFVVISVVPWNDPLLASVGSYQRALELMNIPHAKFLVDMVVLIAVASCMNSSIYI 311 Query: 317 TGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGV-LLNYIVPEQVFVWVTSI 375 RMLY+L + G AP+A SS VP A+ ++ ++G GV L +Y +P +F ++ + Sbjct: 312 ASRMLYSLGRRGDAPKALKVTSSAGVPRSAV-IASTVLGAGVTLFSYFMPAGLFQFLLAS 370 Query: 376 SLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLDP 435 S +L + +I I+ L R+ + ++ + FRM P+ WLV+ F+ A ++ + P Sbjct: 371 SGAIALLVYLVIAISQLRMRRMLQRQNIE-LPFRMWLFPWLTWLVIVFISAALAVMMVTP 429 Query: 436 GTR 438 R Sbjct: 430 EHR 432 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: 682 Number of extensions: 42 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: 466 Length adjustment: 33 Effective length of query: 439 Effective length of database: 433 Effective search space: 190087 Effective search space used: 190087 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