Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate AO356_29455 AO356_29455 amino acid transporter
Query= uniprot:A0A0C4YRF7 (472 letters) >lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_29455 AO356_29455 amino acid transporter Length = 484 Score = 385 bits (990), Expect = e-111 Identities = 198/450 (44%), Positives = 284/450 (63%), Gaps = 4/450 (0%) Query: 15 EEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRAL 74 E+ L R L +RHIQ++A+GGAIG GLF+G+G+ IA++G ++L Y I G+ ++F+MRA+ Sbjct: 10 EQPALQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGLFVYFVMRAM 69 Query: 75 GELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVP 134 GE+LL +FA +A ++GP A F GWSYW W V + + V + YWFPDVP Sbjct: 70 GEMLLSNLNFKTFADFAGAYLGPRAAFFLGWSYWLSWSVAVIGDAVVVGGFFQYWFPDVP 129 Query: 135 QWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFG-VTPLGPT 193 WIPA+ L L+ +N + V +FGE+EFWFA+IK++ +V +I + L +I V+P G T Sbjct: 130 AWIPAIGMLMTLFALNVLTVRLFGEIEFWFAIIKIIAVVTLIGVSLVLIASSFVSPSGVT 189 Query: 194 ASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVW 253 AS ++L P G G Q+ +F++ G ELIG A E +NPEK LP A N + Sbjct: 190 ASLNHLLDKQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRNPEKTLPKAINSIPL 249 Query: 254 RILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSG 313 RI++FYV AL ++A+ W ++ P SPFV +F G P AA IVN VV+T+AASS NSG Sbjct: 250 RIILFYVLALACIIAVTSWQQVSPSKSPFVELFLVAGFPAAAGIVNFVVLTSAASSANSG 309 Query: 314 IFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPE--QVFVW 371 +FS+ RML+ LA AP F R+S VP +++ F+ LM +GVLL +IVPE F Sbjct: 310 VFSSSRMLFGLANQDNAPGIFRRLSGNSVPLLSLAFTTLLMLVGVLLLFIVPEVMTAFTI 369 Query: 372 VTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLL 431 V+++S + ++TWS I+ +++ YRK K+ A++MPG W +AF+ V LL Sbjct: 370 VSTVSAILVIFTWSTILASYIAYRKKRPELHAKS-AYKMPGGVPMAWFSLAFLGFVLCLL 428 Query: 432 SLDPGTRVALYVAPVWFALLGIGYRFTKSR 461 +L P TR+AL V P WF L I Y+ T +R Sbjct: 429 ALRPDTRIALLVMPGWFIWLAIAYQLTDAR 458 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: 703 Number of extensions: 29 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: 484 Length adjustment: 34 Effective length of query: 438 Effective length of database: 450 Effective search space: 197100 Effective search space used: 197100 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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