Align SSS sodium solute transporter (characterized, see rationale)
to candidate CA265_RS19720 CA265_RS19720 sodium transporter
Query= uniprot:L0FZT5 (624 letters) >FitnessBrowser__Pedo557:CA265_RS19720 Length = 558 Score = 445 bits (1144), Expect = e-129 Identities = 250/573 (43%), Positives = 358/573 (62%), Gaps = 60/573 (10%) Query: 7 TLDYVIFIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANISAEH 66 T DY++F +Y + + + GL++ KK +++YFLA+ SLTWWA+GASL+A+NISAE Sbjct: 8 TKDYIVFAIYFVIVAAYGLYIYNKKKSASTGSKDYFLAEGSLTWWAIGASLIASNISAEQ 67 Query: 67 FIGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFNKGVSTA 126 FIG SGSGF +GL I+ YEW+AA+ L+IVA +F+P++LK+ + TMPQFL +R+N V+ Sbjct: 68 FIGMSGSGFKMGLAIATYEWMAALTLVIVAVFFIPVYLKNKIATMPQFLHQRYNGTVAMI 127 Query: 127 FAVFWLLVYVFVNLTSVSYLGALALDKIMGIPLQYGIIGLLIFSGIYSIYGGLEAVAWTD 186 AVFWLL+YV VNLTS+ YLGALA+ I G L + + + F+ + ++ GG++ + +TD Sbjct: 128 MAVFWLLLYVVVNLTSILYLGALAVSSISGFDLTFCMYAIAAFAIVITL-GGMKVIGYTD 186 Query: 187 VVQVIILVAGGLITTFLALDAVGM---GDGIFAGMSNLYNDAKDHFVMIMPQGRVMVPDG 243 V+QV L+ GGL TT+LAL+ V GIF G S + + A +HF MI+ PD Sbjct: 187 VIQVFFLILGGLATTYLALNLVSTHYGTSGIFEGYSLMTSKASEHFHMILK------PD- 239 Query: 244 LGGSRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAGYLKL 303 + + DLPGL+V++GGMW+ NL YWG NQYI Q+ L A ++ A+ G+LFA +LKL Sbjct: 240 ----NENYIDLPGLSVLVGGMWIVNLNYWGCNQYITQRALGA-DLKTARGGILFAAFLKL 294 Query: 304 LMPIIVVIPGIAAYVLIND--YSPEQLAAILNMPVEHIGTIQKSDEAYPWLLRNFIPNGI 361 LMPIIVV+PGIAAYVL D + E L G++ D AYP LL N +P G+ Sbjct: 295 LMPIIVVLPGIAAYVLYKDGAFQSEML---------QDGSV-NPDRAYPVLL-NLLPAGL 343 Query: 362 RGLAFAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVAVVALAIA 421 +GL+FAAL AA+V+SLA NS +TIFT+DIYK K +A+ LV TG+I VVA+ + Sbjct: 344 KGLSFAALTAAVVASLAGKANSIATIFTLDIYKKVLKTDASEKNLVFTGKIAVVVAMVLG 403 Query: 422 MIVAPQLASLDQV--FQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAIATIPAGI 479 +++AP L +D+ FQYIQEYTG++ PG+ +F +G W++AT++AAL+ + + Sbjct: 404 VVIAPYL-GIDKKGGFQYIQEYTGFVSPGIFAMFILGFFWKRATSNAALFATVGGFGLSL 462 Query: 480 VFKIF---------------------YPEMPFLLRMGYVFIILCFIASLISFAEKKKFAN 518 + K+ E+PFL RMG+VF+ +IS E + N Sbjct: 463 LLKVLPTWTDLSWLSGMGFSVKNGVGVYEIPFLDRMGFVFVFCVIGMVIISLFENRNGVN 522 Query: 519 P-----DYKTNKQAAKTVASSYFFIILGIICAV 546 P D K K S II+G++ A+ Sbjct: 523 PKGLEIDSKMFKTTTGFAVGS--LIIIGLLVAL 553 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: 1120 Number of extensions: 58 Number of successful extensions: 11 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 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