Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate Pf1N1B4_4976 D-serine/D-alanine/glycine transporter
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4976 Length = 473 Score = 387 bits (995), Expect = e-112 Identities = 199/454 (43%), Positives = 290/454 (63%), Gaps = 6/454 (1%) Query: 13 VHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMR 72 + E+ L R L +RHIQ++A+GGAIG GLF+G+G+ IA++G ++L Y I G+ ++F+MR Sbjct: 8 ITEQAVLQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGLFVYFVMR 67 Query: 73 ALGELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPD 132 A+GELLL SFA +A ++GP A F GWSYW W V + + V + YWFPD Sbjct: 68 AMGELLLSNLNFKSFADFAGAYLGPRAAFFLGWSYWLSWSVAVVGDAVVVGGFFQYWFPD 127 Query: 133 VPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFG-VTPLG 191 VP WIPA+ + L+ +N + V +FGE+EFWFA+IK++ +VA+I + + +I V+P G Sbjct: 128 VPAWIPAIGMMLTLFALNVLTVKLFGEVEFWFAIIKIIAVVALISVSVLLIASSFVSPTG 187 Query: 192 PTASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGV 251 TAS ++L P G G Q+ +F++ G ELIG A E ++PEK LP A N + Sbjct: 188 VTASLTHLLDKQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRSPEKTLPKAINSI 247 Query: 252 VWRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCN 311 RI++FYV +L+ ++A+ W ++ P SPFV +F G P AA IVN VV+T+AASS N Sbjct: 248 PLRIILFYVLSLVCIIAVTSWQQVSPNKSPFVELFLIAGFPAAAGIVNFVVLTSAASSAN 307 Query: 312 SGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPE--QVF 369 SG+FS+ RML+ LA G AP F R+S VP I++ F+ LM +GVLL +I+PE F Sbjct: 308 SGVFSSSRMLFGLADLGNAPGIFRRLSKNSVPLISLAFTTFLMLLGVLLLFIIPEVMTAF 367 Query: 370 VWVTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAV 429 V+++S + ++TWS I+ +++ YRKA ++ ++MPG W +AF+ V Sbjct: 368 TIVSTVSAILVIFTWSTILASYIAYRKARPDLHAQS-RYKMPGGVPMAWFSLAFLAFVLC 426 Query: 430 LLSLDPGTRVALYVAPVWFALLGIGYRFT--KSR 461 LL+L P TR+AL V P WF L I Y+F+ KSR Sbjct: 427 LLALRPDTRLALCVMPAWFIWLAIAYQFSHFKSR 460 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: 673 Number of extensions: 29 Number of successful extensions: 4 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: 473 Length adjustment: 33 Effective length of query: 439 Effective length of database: 440 Effective search space: 193160 Effective search space used: 193160 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