Align SSS sodium solute transporter (characterized, see rationale)
to candidate CA265_RS06130 CA265_RS06130 sodium transporter
Query= uniprot:L0FZT5 (624 letters) >FitnessBrowser__Pedo557:CA265_RS06130 Length = 558 Score = 437 bits (1123), Expect = e-127 Identities = 251/578 (43%), Positives = 355/578 (61%), Gaps = 57/578 (9%) Query: 7 TLDYVIFIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANISAEH 66 T DY++F +Y + + + GL++ KK +++YFLA+ SLTWWA+GASL+A+NISAE Sbjct: 8 TKDYIVFAIYFVIVAAYGLYIYNKKKSESTGSKDYFLAEGSLTWWAIGASLIASNISAEQ 67 Query: 67 FIGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFNKGVSTA 126 FIG SGSGF +GL I+ YEW+ A L++VA +F+P++LK+ + TMPQFL +R+N V+ Sbjct: 68 FIGMSGSGFKMGLAIATYEWMGAATLVVVAVFFIPVYLKNKIATMPQFLHQRYNGTVAMI 127 Query: 127 FAVFWLLVYVFVNLTSVSYLGALALDKIMGIPLQYGIIGLLIFSGIYSIYGGLEAVAWTD 186 AVFWLL+YV VNLTS+ YLGALA+ I G L + + + F+ I ++ GG++ + +TD Sbjct: 128 MAVFWLLLYVVVNLTSILYLGALAVSSISGFDLSFCMYAIAGFAIIITL-GGMKVIGYTD 186 Query: 187 VVQVIILVAGGLITTFLALDAVGM---GDGIFAGMSNLYNDAKDHFVMIMPQGRVMVPDG 243 V+QV L+ GGL TT+LAL+ V GIF G S + + A +HF MI Sbjct: 187 VIQVFFLILGGLATTYLALNLVSTHYGTTGIFEGYSLMTSKASEHFHMI----------- 235 Query: 244 LGGSRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAGYLKL 303 L + + DLPGL+V++GGMW+ NL YWG NQYI Q+ L A ++E A+ G+LFA +LKL Sbjct: 236 LKPENENYIDLPGLSVLVGGMWIVNLNYWGCNQYITQRALGA-NLETARGGILFAAFLKL 294 Query: 304 LMPIIVVIPGIAAYVLIND--YSPEQLAAILNMPVEHIGTIQKSDEAYPWLLRNFIPNGI 361 LMPIIVV+PGIAAYVL D + E L G + D AYP LL N +P G+ Sbjct: 295 LMPIIVVLPGIAAYVLFKDGAFQSEML---------QDGAV-NPDRAYPVLL-NLLPAGL 343 Query: 362 RGLAFAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVAVVALAIA 421 +GL+FAAL AA+V+SLA NS +TIFT+DIYK + +A LV TG+I +VA+ + Sbjct: 344 KGLSFAALTAAVVASLAGKANSIATIFTLDIYKKVLRTDATEKNLVTTGKISIIVAMILG 403 Query: 422 MIVAPQLASLDQV--FQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAIATIPAGI 479 +++AP L +D+ FQYIQEYTG++ PG+ +F +G W++ T++AAL+ I I Sbjct: 404 VLIAPHL-GIDKKGGFQYIQEYTGFVSPGIFAMFILGFFWKRTTSTAALFATIGGFGLSI 462 Query: 480 VFKIFYP----------------------EMPFLLRMGYVFIILCFIASLISFAEKKKFA 517 + K F P E+PFL RMG+VF+ +IS K A Sbjct: 463 LLK-FLPNLTDLSWLSGMGFSVKNAAGVYEIPFLDRMGFVFVFCIIGMYIISMLSNK--A 519 Query: 518 NPDYKTNKQAAKTVASSYFFIILGIICAVLGFALFNSY 555 + K AK +S F + +I L AL++ Y Sbjct: 520 EAEAKGLAIDAKMFKTSTSFAVGALIIIGLLVALYSVY 557 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: 1114 Number of extensions: 56 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 624 Length of database: 558 Length adjustment: 37 Effective length of query: 587 Effective length of database: 521 Effective search space: 305827 Effective search space used: 305827 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 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