Align SSS sodium solute transporter (characterized, see rationale)
to candidate 5210844 Shew_3270 SSS family solute/sodium (Na+) symporter (RefSeq)
Query= uniprot:L0FZF3 (547 letters) >FitnessBrowser__PV4:5210844 Length = 474 Score = 228 bits (581), Expect = 4e-64 Identities = 154/501 (30%), Positives = 254/501 (50%), Gaps = 50/501 (9%) Query: 5 TLDLVVFVAYCLLIITMGIVVSREKKGHVKDSKDYFLASKALPWWAVGASLIASNISAEQ 64 T+ + +FVA L+ + + R+ DS+DYFLA L W V SL+ +NISAEQ Sbjct: 4 TIQVAIFVALTTLVALITYLKCRKVTRDANDSRDYFLAGGGLSWIVVAGSLMMTNISAEQ 63 Query: 65 FIGMSGSGFALGLAISTYEWMAAATLLVVAIFFLPIYLKEGIYTMPQFLNRRY-DGRVRT 123 +GM+G A L ++ +E AA L+++A + +PIY + T + L R+Y D +R Sbjct: 64 IVGMNG---AQTLLVAWWEIAAAIGLIILAKWLIPIYYRYNCTTTTELLERKYQDKGIRA 120 Query: 124 VMAIFWLLIYVFVNLTSVLYLGALSLETIMGVPLTYGIIGL--ALFAMVYSIYGGLKAVA 181 ++++ ++L Y F+ L VLY G+L ++++ G+ ++ ++ + A+ +Y+I+GGL+A+A Sbjct: 121 MVSLLFMLGYAFILLPVVLYTGSLFMKSMFGLSISVTVLAIIFAVVGAIYAIFGGLRAIA 180 Query: 182 WTDVVQVVFLVAGGLATTYLALSLVGDGDVWEGIGILRKAAPSHFSMIIEKGEMMIPDGS 241 +D + + L+ GLA +YLA+ V W+ GI P +I + IP Sbjct: 181 ISDTLNGLGLILMGLAVSYLAMHAVD----WDLSGI-----PLERLTLIGDSQSDIP--- 228 Query: 242 GGSRDAYLDLPGLSVLIGGMWIVNLNYWGCNQYITQRALAAKSLGEAQTGMVFAGFLKLL 301 S L+ GM + + YWG N ITQRALAAKS+ EAQ G+ A +KL+ Sbjct: 229 ------------WSTLLTGMIFIQIFYWGTNMVITQRALAAKSVKEAQKGLYAAVVMKLI 276 Query: 302 MPLIVVIPGIAAYVIVQKGADASFIESMTDPVTGLAKSDRAYPTLLHLLPPGLKGLAFAA 361 +P+IVV+PGI A+ + D ++ + + D LLP L G A Sbjct: 277 IPVIVVLPGIVAFKLYGDVGDVAYGKLVGD-----------------LLPSWLSGAFAAV 319 Query: 362 LTAAIVSSLASMANSTSTIFTIDIYKEFFNKNVSEGKQVTIGRITAVVAFIIAAIVAPQL 421 + A++SS S NS + ++T DI++ + N + K IG A++ +I+ + P Sbjct: 320 IAGAVLSSFNSCLNSAAALYTCDIHQNYINADADVRK---IGSRVALLFTLISVALVPLF 376 Query: 422 RQLDQAFQYIQEYTGFVSPGVFAIFIFGFFWKKTTSNAALTAAVLTIPLSAAFKVITPNL 481 + + +Q+ G S V A FI +K ++ A V + L A F I L Sbjct: 377 ARSESIIALLQQLNGLYSMPVLAAFICALVFKNVSAKAIKWGLVFGVLLYALFTFIWSPL 436 Query: 482 PFIDRMGVVFLVLSVLIIAIS 502 FI M + L ++ + S Sbjct: 437 HFIHLMAITLLATILVTLVFS 457 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: 631 Number of extensions: 37 Number of successful extensions: 6 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: 474 Length adjustment: 34 Effective length of query: 513 Effective length of database: 440 Effective search space: 225720 Effective search space used: 225720 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