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

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_RS19720 CA265_RS19720 sodium transporter

Query= uniprot:A0A1X9Z2P8
         (558 letters)



>FitnessBrowser__Pedo557:CA265_RS19720
          Length = 558

 Score = 1019 bits (2635), Expect = 0.0
 Identities = 511/558 (91%), Positives = 536/558 (96%)

Query: 1   MKNNLLDTKDYIVFAIYFVIVAAYGLYIYNKKKSESTGSKDYFLAEGSLTWWAIGASLIA 60
           MKNNLLDTKDYIVFAIYFVIVAAYGLYIYNKKKS STGSKDYFLAEGSLTWWAIGASLIA
Sbjct: 1   MKNNLLDTKDYIVFAIYFVIVAAYGLYIYNKKKSASTGSKDYFLAEGSLTWWAIGASLIA 60

Query: 61  SNISAEQFIGMSGSGFKMGLAIATYEWMGAATLVVVAVFFIPVYLKNKIATMPQFLHQRY 120
           SNISAEQFIGMSGSGFKMGLAIATYEWM A TLV+VAVFFIPVYLKNKIATMPQFLHQRY
Sbjct: 61  SNISAEQFIGMSGSGFKMGLAIATYEWMAALTLVIVAVFFIPVYLKNKIATMPQFLHQRY 120

Query: 121 NGTVAMIMAVFWLLLYVVVNLTSILYLGALAVSSISGFDLSFCMYAIAGFAIIITLGGMK 180
           NGTVAMIMAVFWLLLYVVVNLTSILYLGALAVSSISGFDL+FCMYAIA FAI+ITLGGMK
Sbjct: 121 NGTVAMIMAVFWLLLYVVVNLTSILYLGALAVSSISGFDLTFCMYAIAAFAIVITLGGMK 180

Query: 181 VIGYTDVIQVFFLILGGLATTYLALNLVSTHYGTTGIFEGYSLMTSKASEHFHMILKPEN 240
           VIGYTDVIQVFFLILGGLATTYLALNLVSTHYGT+GIFEGYSLMTSKASEHFHMILKP+N
Sbjct: 181 VIGYTDVIQVFFLILGGLATTYLALNLVSTHYGTSGIFEGYSLMTSKASEHFHMILKPDN 240

Query: 241 ENYIDLPGLSVLVGGMWIVNLNYWGCNQYITQRALGANLETARGGILFAAFLKLLMPIIV 300
           ENYIDLPGLSVLVGGMWIVNLNYWGCNQYITQRALGA+L+TARGGILFAAFLKLLMPIIV
Sbjct: 241 ENYIDLPGLSVLVGGMWIVNLNYWGCNQYITQRALGADLKTARGGILFAAFLKLLMPIIV 300

Query: 301 VLPGIAAYVLFKDGAFQSEMLQDGAVNPDRAYPVLLNLLPAGLKGLSFAALTAAVVASLA 360
           VLPGIAAYVL+KDGAFQSEMLQDG+VNPDRAYPVLLNLLPAGLKGLSFAALTAAVVASLA
Sbjct: 301 VLPGIAAYVLYKDGAFQSEMLQDGSVNPDRAYPVLLNLLPAGLKGLSFAALTAAVVASLA 360

Query: 361 GKANSIATIFTLDIYKKVLRTDATEKNLVTTGKISIIVAMILGVLIAPHLGIDKKGGFQY 420
           GKANSIATIFTLDIYKKVL+TDA+EKNLV TGKI+++VAM+LGV+IAP+LGIDKKGGFQY
Sbjct: 361 GKANSIATIFTLDIYKKVLKTDASEKNLVFTGKIAVVVAMVLGVVIAPYLGIDKKGGFQY 420

Query: 421 IQEYTGFVSPGIFAMFILGFFWKRTTSTAALFATIGGFGLSILLKFLPNLTDLSWLSGMG 480
           IQEYTGFVSPGIFAMFILGFFWKR TS AALFAT+GGFGLS+LLK LP  TDLSWLSGMG
Sbjct: 421 IQEYTGFVSPGIFAMFILGFFWKRATSNAALFATVGGFGLSLLLKVLPTWTDLSWLSGMG 480

Query: 481 FSVKNAAGVYEIPFLDRMGFVFVFCIIGMYIISMLSNKAEAEAKGLAIDAKMFKTSTSFA 540
           FSVKN  GVYEIPFLDRMGFVFVFC+IGM IIS+  N+     KGL ID+KMFKT+T FA
Sbjct: 481 FSVKNGVGVYEIPFLDRMGFVFVFCVIGMVIISLFENRNGVNPKGLEIDSKMFKTTTGFA 540

Query: 541 VGALIIIGLLVALYSVYW 558
           VG+LIIIGLLVALYSVYW
Sbjct: 541 VGSLIIIGLLVALYSVYW 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: 1276
Number of extensions: 48
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources