Align SSS sodium solute transporter (characterized, see rationale)
to candidate 3610523 Dshi_3904 SSS sodium solute transporter superfamily (RefSeq)
Query= uniprot:L0FZF3 (547 letters) >FitnessBrowser__Dino:3610523 Length = 526 Score = 241 bits (614), Expect = 7e-68 Identities = 165/558 (29%), Positives = 267/558 (47%), Gaps = 59/558 (10%) Query: 6 LDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISAEQF 65 LD V Y ++I +G+ V+R+ + +D FLA ++L W A+G SL ASNIS Sbjct: 12 LDYGVIAVYLAIVIAIGVWVARK----TRTGEDLFLAGRSLGWAAIGFSLFASNISTSTL 67 Query: 66 IGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRYDGRVRTVM 125 +G++GS + GL +S+YEWMA LL +A F P++LK I T P++L RY RVR Sbjct: 68 VGLTGSAYTGGLTVSSYEWMAGIPLLFMAFIFAPVFLKSRISTTPEYLENRYSRRVRLYF 127 Query: 126 AIFWLLIYVFVNLTSVLYLGALSLETIM-GVPLTYGIIGLALFAMVYSIYGGLKAVAWTD 184 + ++ V V+ LY GA+ L+ + + + + LFA +Y+ GGL+AV +TD Sbjct: 128 SGLTIVFTVIVDTAGGLYAGAVVLKVFFPDLDIWMSCVAIGLFAGIYTATGGLRAVVYTD 187 Query: 185 VVQVVFLVAGGLATTYLALSLVGDGDVWEGIGILRKAAPSHFSMIIEKGEMMIPDGSGGS 244 ++Q V L+ G T +L V WE + R P I++ + Sbjct: 188 ILQAVVLICGTGLTAFLMYQSVDFS--WESV---RSQVPEGHLSIVQPID---------- 232 Query: 245 RDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLKLLMPL 304 D L PG L G+W++ YW NQYI QR L AK L AQ G + G LK+L Sbjct: 233 -DDTLPWPG---LFTGVWLLGFWYWVTNQYIVQRVLGAKDLSNAQWGAILGGILKILPTF 288 Query: 305 IVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTLL-HLLPPGLKGLAFAALT 363 +++PG+ A V + + SD+ +P ++ +LP GL GL A L Sbjct: 289 FIILPGVMALV----------------TLPDIQNSDQVFPIIITEVLPSGLTGLVMAGLI 332 Query: 364 AAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGR--ITAVVAFIIAAIV-APQ 420 AAI+S++ S NS+ST+ + +F + E T + + A + F++ AI AP Sbjct: 333 AAIMSTVDSTLNSSSTL----LINDFLTRPEKEPDPETAKKWGMMATLGFMVIAIAWAPL 388 Query: 421 LRQLDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLSAAFKVITP- 479 ++ + YIQ+ + P + F G W + T NAA ++ L ++ Sbjct: 389 IQYFGGLWAYIQQAFSVLVPPLVVCFTLGALWSRGTENAAFWTLIIGHTLGLVVFMLNQF 448 Query: 480 ---NLPFIDRMGVVFLVLSVLIIAISLYEGKGKDSKKAIEVDAELFSTST-------KFK 529 L + + ++ V + + +A+SL + + A+ A+ F T K Sbjct: 449 GIWPLHYTISVTIMTAVSAAIFVALSLRDDTPDVREDALWQRADAFDTPATTAPVLKNVK 508 Query: 530 VGAVLICGILVALYSVFW 547 A+L+ +++ +FW Sbjct: 509 THAILLILLMIGTLVLFW 526 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: 756 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: 547 Length of database: 526 Length adjustment: 35 Effective length of query: 512 Effective length of database: 491 Effective search space: 251392 Effective search space used: 251392 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: 52 (24.6 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