Align SSS sodium solute transporter (characterized, see rationale)
to candidate 17739 b3679 predicted transporter (NCBI)
Query= uniprot:L0FZF3 (547 letters) >FitnessBrowser__Keio:17739 Length = 571 Score = 231 bits (588), Expect = 7e-65 Identities = 168/558 (30%), Positives = 275/558 (49%), Gaps = 55/558 (9%) Query: 4 NTLDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISAE 63 N+L ++ FV + LL+ I + +K + YFLA ++L + ASL+ +N+S E Sbjct: 2 NSLQILSFVGFTLLVAV--ITWWKVRKTDTGSQQGYFLAGRSLKAPVIAASLMLTNLSTE 59 Query: 64 QFIGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGRVRT 123 Q +G+SG + G+++ +E +A TL+ +A+ FLP YLK GI T+P FL RYD R Sbjct: 60 QLVGLSGQAYKSGMSVMGWEVTSAVTLIFLALIFLPRYLKRGIATIPDFLEERYDKTTRI 119 Query: 124 VMAIFWLLIYVFVNLTSVLYLGALSLETIMGV----PLTYG------IIGLALFAMVYSI 173 ++ +L+ L VLY GAL+L ++ V +++G +I L L ++Y++ Sbjct: 120 IIDFCFLIATGVCFLPIVLYSGALALNSLFHVGESLQISHGAAIWLLVILLGLAGILYAV 179 Query: 174 YGGLKAVAWTDVVQVVFLVAGGLATTYLALSLVGDGDVWEGIGILRKAAPSHFSMIIEKG 233 GGL+A+A D + + LV GGL L +G G +GI L + I Sbjct: 180 IGGLRAMAVADSINGIGLVIGGLMVPVFGLIAMGKGSFMQGIEQLTTVHAEKLNSI---- 235 Query: 234 EMMIPDGSGGSRDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMV 293 GG D LP + G+ +VN YW NQ I QR LA+KSL E Q G + Sbjct: 236 --------GGPTD---PLP-IGAAFTGLILVNTFYWCTNQGIVQRTLASKSLAEGQKGAL 283 Query: 294 FAGFLKLLMPLIVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTLL-HLLPP 352 LK+L PL++V+PG+ A+ + Q L K+D AYPTL+ ++LP Sbjct: 284 LTAVLKMLDPLVLVLPGLIAFHLYQ----------------DLPKADMAYPTLVNNVLPV 327 Query: 353 GLKGLAFAALTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFI 412 + G A L A++S+ NS ST+F++ IY+ N+N + VT+GR I Sbjct: 328 PMVGFFGAVLFGAVISTFNGFLNSASTLFSMGIYRRIINQNAEPQQLVTVGRKFGFFIAI 387 Query: 413 IAAIVAPQLRQLDQA-FQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLS 471 ++ +VAP + Q + ++++ G + + I I GFF+ + + AA A + I Sbjct: 388 VSVLVAPWIANAPQGLYSWMKQLNGIYNVPLVTIIIMGFFFPRIPALAAKVAMGIGIISY 447 Query: 472 AAFKVITP-NLPFIDRMGVVFLVLSVLIIAISLYEGKGK--DSKKAIEVDAELFSTSTKF 528 + + F+ + F + V+++ I + + K A VD + + Sbjct: 448 ITINYLVKFDFHFLYVLACTFCINVVVMLVIGFIKPRATPFTFKDAFAVDMKPWK---NV 504 Query: 529 KVGAVLICGILVALYSVF 546 K+ ++ GIL A+ V+ Sbjct: 505 KIASI---GILFAMIGVY 519 Lambda K H 0.326 0.140 0.414 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: 760 Number of extensions: 39 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: 547 Length of database: 571 Length adjustment: 36 Effective length of query: 511 Effective length of database: 535 Effective search space: 273385 Effective search space used: 273385 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 (21.6 bits) S2: 53 (25.0 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