Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate 1937132 b3795 predicted transporter (NCBI)
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__Keio:1937132 Length = 461 Score = 440 bits (1131), Expect = e-128 Identities = 215/441 (48%), Positives = 304/441 (68%), Gaps = 3/441 (0%) Query: 18 DLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGEL 77 +L RGL+ RHI++IA+GG IGVGLF+GA + AGP ++L+Y I G+ +FFIMR++GE+ Sbjct: 7 ELQRGLEARHIELIALGGTIGVGLFMGAASTLKWAGPSVLLAYIIAGLFVFFIMRSMGEM 66 Query: 78 LLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWI 137 L PV+GSFA YA ++ PF G+ T WSYWFMW+ G++EITA+ VYV +WFP++ QWI Sbjct: 67 LFLEPVTGSFAVYAHRYMSPFFGYLTAWSYWFMWMAVGISEITAIGVYVQFWFPEMAQWI 126 Query: 138 PALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFS 197 PAL +A++ L N AV ++GE+EFWFA+IKV TI+ MIVIGL +IFFG G + FS Sbjct: 127 PALIAVALVALANLAAVRLYGEIEFWFAMIKVTTIIVMIVIGLGVIFFGFGNGGQSIGFS 186 Query: 198 NLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILI 257 NL HGGF G G + L IV+ +YQGVELIG+TAGEA+NP+ L A V+WRILI Sbjct: 187 NLTEHGGFFAGGWKGFLTALCIVVASYQGVELIGITAGEAKNPQVTLRSAVGKVLWRILI 246 Query: 258 FYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIFST 317 FYVGA+ +++ + PWNE+ SPFV F +IG+ AA I+N VV+TAA S CNSG++S Sbjct: 247 FYVGAIFVIVTIFPWNEIGSNGSPFVLTFAKIGITAAAGIINFVVLTAALSGCNSGMYSC 306 Query: 318 GRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIV--PEQVFVWVTSI 375 GRMLY LA+ Q P A +VS VP + S A++ IG LNYI+ P++VFV+V S Sbjct: 307 GRMLYALAKNRQLPAAMAKVSRHGVPVAGVAVSIAILLIGSCLNYIIPNPQRVFVYVYSA 366 Query: 376 SLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLDP 435 S++ + W +I+I+ L +R+A A + + FR P+AN++ +AF+I V + + + Sbjct: 367 SVLPGMVPWFVILISQLRFRRAHKAA-IASHPFRSILFPWANYVTMAFLICVLIGMYFNE 425 Query: 436 GTRVALYVAPVWFALLGIGYR 456 TR++L+V ++ + Y+ Sbjct: 426 DTRMSLFVGIIFMLAVTAIYK 446 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: 797 Number of extensions: 46 Number of successful extensions: 3 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: 461 Length adjustment: 33 Effective length of query: 439 Effective length of database: 428 Effective search space: 187892 Effective search space used: 187892 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