Align Sodium transporter (characterized, see rationale)
to candidate CA265_RS06755 CA265_RS06755 sodium transporter
Query= uniprot:A0A1X9Z2P8 (558 letters) >FitnessBrowser__Pedo557:CA265_RS06755 Length = 542 Score = 658 bits (1698), Expect = 0.0 Identities = 328/557 (58%), Positives = 424/557 (76%), Gaps = 18/557 (3%) Query: 4 NLLDTKDYIVFAIYFVIVAAYGLYIYNKKKSESTGSKDYFLAEGSLTWWAIGASLIASNI 63 N L DY VF +YFVIV+AYG ++Y KK + T +KDYFLAEGSLTWWAIGAS+IASNI Sbjct: 2 NHLSAFDYAVFLMYFVIVSAYGYWVYRSKKKKRTDTKDYFLAEGSLTWWAIGASIIASNI 61 Query: 64 SAEQFIGMSGSGFKMGLAIATYEWMGAATLVVVAVFFIPVYLKNKIATMPQFLHQRYNGT 123 SAE FIGMSGSGF MGLAIA+YEWM AATL++VA+FF+P+Y+KNKI TMPQFL RYN T Sbjct: 62 SAEHFIGMSGSGFAMGLAIASYEWMAAATLIIVAIFFLPIYIKNKIYTMPQFLSNRYNNT 121 Query: 124 VAMIMAVFWLLLYVVVNLTSILYLGALAVSSISGFDLSFCMYAIAGFAIIITLGGMKVIG 183 V+ +MAVFWLL+YV VNLTSI +LGA+A+ +I+G + C+ +A F+ IITLGGMKVIG Sbjct: 122 VSTLMAVFWLLVYVFVNLTSIFFLGAIAIETITGVPFNICIIFLAIFSAIITLGGMKVIG 181 Query: 184 YTDVIQVFFLILGGLATTYLALNLVSTHYGTTGIFEGYSLMTSKASEHFHMILKPENENY 243 YTDVIQVF L+ GGL T Y+AL LVS + L+ S+AS+HFHMI ++ Y Sbjct: 182 YTDVIQVFVLVAGGLITCYMALKLVSEKLDAPSVLASLPLLRSEASDHFHMIFSKGDKFY 241 Query: 244 IDLPGLSVLVGGMWIVNLNYWGCNQYITQRALGANLETARGGILFAAFLKLLMPIIVVLP 303 +LPG++VLVGG+WI NLNYWGCNQYI QRALGA+L+T R G++FAAFLKLL+P+IVV+P Sbjct: 242 NELPGIAVLVGGLWINNLNYWGCNQYIVQRALGADLKTGRNGLIFAAFLKLLIPVIVVIP 301 Query: 304 GIAAYVLFKDGAFQSEMLQ-DGAVNPDRAYPVLLNLLPAGLKGLSFAALTAAVVASLAGK 362 GIAAYVL++ G F SEML G V PD AYPVL+NLLPAG+KGL+FAALTAA+VASLAGK Sbjct: 302 GIAAYVLYQRGYFHSEMLDAAGVVKPDHAYPVLMNLLPAGIKGLAFAALTAAIVASLAGK 361 Query: 363 ANSIATIFTLDIYKKVLRTDATEKNLVTTGKISIIVAMILGVLIAPHL-GIDKKGGFQYI 421 NSIATIFTLDIYKK ++ +A+E LV+ G+ S+++A ++ ++IAP L D+ +Q+I Sbjct: 362 CNSIATIFTLDIYKKFIKPEASETRLVSVGRWSVVIASLIAIIIAPALRSFDQV--YQFI 419 Query: 422 QEYTGFVSPGIFAMFILGFFWKRTTSTAALFATIGGFGLSILLKFLPNLTDLSWLSGMGF 481 QEY GF+SPG+FA+F+LGFFWK+TTS AAL A + LS L KFLP +T+ Sbjct: 420 QEYVGFISPGVFAIFLLGFFWKKTTSRAALTAALLTIPLSTLFKFLPAVTN--------- 470 Query: 482 SVKNAAGVYEIPFLDRMGFVFVFCIIGMYIISMLSNKAEAEAKGLAIDAKMFKTSTSFAV 541 + IPFL+RM +VF+ I M ++++ K++ +GL ID+ MFK + +F + Sbjct: 471 -----GAIAPIPFLNRMSWVFMIIIGLMIVVTLTDPKSKDNPQGLEIDSSMFKVTPAFTI 525 Query: 542 GALIIIGLLVALYSVYW 558 +++I G+L ALY+V+W Sbjct: 526 ASVMICGILAALYTVFW 542 Lambda K H 0.326 0.141 0.419 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: 898 Number of extensions: 41 Number of successful extensions: 4 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: 558 Length of database: 542 Length adjustment: 36 Effective length of query: 522 Effective length of database: 506 Effective search space: 264132 Effective search space used: 264132 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