GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sglS in Pedobacter sp. GW460-11-11-14-LB5

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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