Align SSS sodium solute transporter (characterized, see rationale)
to candidate CA265_RS04220 CA265_RS04220 sodium:solute symporter
Query= uniprot:L0FZT5 (624 letters) >FitnessBrowser__Pedo557:CA265_RS04220 Length = 550 Score = 273 bits (697), Expect = 2e-77 Identities = 171/518 (33%), Positives = 280/518 (54%), Gaps = 37/518 (7%) Query: 6 STLDYVIFIVYALAIVSVGLWV-SRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANISA 64 ST D VI I Y L IV++GLW +R KK E T+ EYFLA K+L W +G +L A NIS Sbjct: 3 STTDIVITIAYILFIVTIGLWTGTRKKKNEETTSGEYFLAGKTLKWPMIGLALFATNISC 62 Query: 65 EHFIGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFNKGVS 124 H + + SGF GL +EW+AA LI++A F+P +++ G+ T+P FL R+N+ Sbjct: 63 LHLVSLAQSGFDSGLLNGNFEWMAAFTLILLALLFIPFYIRSGISTLPDFLERRYNRACR 122 Query: 125 TAFAVFWLLVYVFVNLTSVSYLGALALDKIMGIPLQYGIIGLLIFSGIYSIYGGLEAVAW 184 A +L + +++ G + L+ + GI + I+ + + +G+Y+I GGL AV Sbjct: 123 DWLAFISILSAIIIHIAFSFLAGGIVLETLFGIDMYVSIVVIALLTGLYTIIGGLRAVVV 182 Query: 185 TDVVQVIILVAGGLITTFLALDAVGMGDGIFAGMSNLYNDAKDHFVMIMPQGRVMVPDGL 244 T+ +Q ++L+ G +I T+ A + VG D + A + +A D MI P G D Sbjct: 183 TETIQSLVLITGAIIITYFAWNKVGGWDHMTAILQK--ENAMDKLSMIRPIG-----DKS 235 Query: 245 GGSRDAFQDLPGLAVILG----GMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAGY 300 G + +AV LG G+W YW +Q I+Q+ L AK A+ G LF G+ Sbjct: 236 G--------MSWIAVFLGYPVLGIW-----YWCADQTIVQRVLGAKDENHARVGSLFCGF 282 Query: 301 LKLLMPIIVVIPGIAAYVLINDYSPEQLAAILNMPVEHIGTIQKSDEAYPWLLRNFIPNG 360 +K+L I V+PG+ AY+L + + + L + T+ + Y ++ +P G Sbjct: 283 IKILPVFIFVLPGLFAYILYKSGTMD--LSSLQTVGSNGETVLNTKGIYTLMITQLLPKG 340 Query: 361 IRGLAFAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVAVVALAI 420 + G+ AAL + ++S +A +NS +T+ + D+YK FKP ++ +LV GR A +AL + Sbjct: 341 LVGILVAALLSGLMSQIAGALNSIATLSSYDLYK-RFKPETSDKKLVSVGRWSAGIALTV 399 Query: 421 AMIVAPQLASLDQVFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAI--ATIPAG 478 ++ + P L S + +F I + +I P + VF +G+ W++A+A A +T + + I AG Sbjct: 400 SIGLLPLLNSYESLFNGINDVIAHIAPPITCVFLLGVFWKKASAKGAQYTLLLGSIIGAG 459 Query: 479 --IVFKIFYPE-----MPFLLRMGYVFIILCFIASLIS 509 +V K++ E +PF++ Y+F I I + S Sbjct: 460 VFVVNKVYGTETIIGQIPFMMMAFYLFCICVLIQVVFS 497 Lambda K H 0.327 0.142 0.427 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: 954 Number of extensions: 55 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: 624 Length of database: 550 Length adjustment: 37 Effective length of query: 587 Effective length of database: 513 Effective search space: 301131 Effective search space used: 301131 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 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. 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