Align Sodium transporter (characterized, see rationale)
to candidate CA265_RS06130 CA265_RS06130 sodium transporter
Query= uniprot:A0A1X9Z2P8 (558 letters) >FitnessBrowser__Pedo557:CA265_RS06130 Length = 558 Score = 1091 bits (2822), Expect = 0.0 Identities = 558/558 (100%), Positives = 558/558 (100%) Query: 1 MKNNLLDTKDYIVFAIYFVIVAAYGLYIYNKKKSESTGSKDYFLAEGSLTWWAIGASLIA 60 MKNNLLDTKDYIVFAIYFVIVAAYGLYIYNKKKSESTGSKDYFLAEGSLTWWAIGASLIA Sbjct: 1 MKNNLLDTKDYIVFAIYFVIVAAYGLYIYNKKKSESTGSKDYFLAEGSLTWWAIGASLIA 60 Query: 61 SNISAEQFIGMSGSGFKMGLAIATYEWMGAATLVVVAVFFIPVYLKNKIATMPQFLHQRY 120 SNISAEQFIGMSGSGFKMGLAIATYEWMGAATLVVVAVFFIPVYLKNKIATMPQFLHQRY Sbjct: 61 SNISAEQFIGMSGSGFKMGLAIATYEWMGAATLVVVAVFFIPVYLKNKIATMPQFLHQRY 120 Query: 121 NGTVAMIMAVFWLLLYVVVNLTSILYLGALAVSSISGFDLSFCMYAIAGFAIIITLGGMK 180 NGTVAMIMAVFWLLLYVVVNLTSILYLGALAVSSISGFDLSFCMYAIAGFAIIITLGGMK Sbjct: 121 NGTVAMIMAVFWLLLYVVVNLTSILYLGALAVSSISGFDLSFCMYAIAGFAIIITLGGMK 180 Query: 181 VIGYTDVIQVFFLILGGLATTYLALNLVSTHYGTTGIFEGYSLMTSKASEHFHMILKPEN 240 VIGYTDVIQVFFLILGGLATTYLALNLVSTHYGTTGIFEGYSLMTSKASEHFHMILKPEN Sbjct: 181 VIGYTDVIQVFFLILGGLATTYLALNLVSTHYGTTGIFEGYSLMTSKASEHFHMILKPEN 240 Query: 241 ENYIDLPGLSVLVGGMWIVNLNYWGCNQYITQRALGANLETARGGILFAAFLKLLMPIIV 300 ENYIDLPGLSVLVGGMWIVNLNYWGCNQYITQRALGANLETARGGILFAAFLKLLMPIIV Sbjct: 241 ENYIDLPGLSVLVGGMWIVNLNYWGCNQYITQRALGANLETARGGILFAAFLKLLMPIIV 300 Query: 301 VLPGIAAYVLFKDGAFQSEMLQDGAVNPDRAYPVLLNLLPAGLKGLSFAALTAAVVASLA 360 VLPGIAAYVLFKDGAFQSEMLQDGAVNPDRAYPVLLNLLPAGLKGLSFAALTAAVVASLA Sbjct: 301 VLPGIAAYVLFKDGAFQSEMLQDGAVNPDRAYPVLLNLLPAGLKGLSFAALTAAVVASLA 360 Query: 361 GKANSIATIFTLDIYKKVLRTDATEKNLVTTGKISIIVAMILGVLIAPHLGIDKKGGFQY 420 GKANSIATIFTLDIYKKVLRTDATEKNLVTTGKISIIVAMILGVLIAPHLGIDKKGGFQY Sbjct: 361 GKANSIATIFTLDIYKKVLRTDATEKNLVTTGKISIIVAMILGVLIAPHLGIDKKGGFQY 420 Query: 421 IQEYTGFVSPGIFAMFILGFFWKRTTSTAALFATIGGFGLSILLKFLPNLTDLSWLSGMG 480 IQEYTGFVSPGIFAMFILGFFWKRTTSTAALFATIGGFGLSILLKFLPNLTDLSWLSGMG Sbjct: 421 IQEYTGFVSPGIFAMFILGFFWKRTTSTAALFATIGGFGLSILLKFLPNLTDLSWLSGMG 480 Query: 481 FSVKNAAGVYEIPFLDRMGFVFVFCIIGMYIISMLSNKAEAEAKGLAIDAKMFKTSTSFA 540 FSVKNAAGVYEIPFLDRMGFVFVFCIIGMYIISMLSNKAEAEAKGLAIDAKMFKTSTSFA Sbjct: 481 FSVKNAAGVYEIPFLDRMGFVFVFCIIGMYIISMLSNKAEAEAKGLAIDAKMFKTSTSFA 540 Query: 541 VGALIIIGLLVALYSVYW 558 VGALIIIGLLVALYSVYW Sbjct: 541 VGALIIIGLLVALYSVYW 558 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: 1329 Number of extensions: 45 Number of successful extensions: 1 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: 558 Length adjustment: 36 Effective length of query: 522 Effective length of database: 522 Effective search space: 272484 Effective search space used: 272484 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