GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctQ in Shewanella sp. ANA-3

Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), small permease component (characterized)
to candidate 7024208 Shewana3_1415 tripartite ATP-independent periplasmic transporter DctQ (RefSeq)

Query= reanno::PV4:5208944
         (212 letters)



>FitnessBrowser__ANA3:7024208
          Length = 214

 Score =  311 bits (796), Expect = 7e-90
 Identities = 147/212 (69%), Positives = 174/212 (82%)

Query: 1   MMSRFFSHIEEVVLNALITAMTLLVFVEVIARFFFNTGFLWIQELTLTICGWFVLFGMSY 60
           M+SR F + EE VLN LIT MTLLVF EV+ARFFFNTGFLWIQELTLT+CGWFVLFGMSY
Sbjct: 1   MISRIFGYFEEGVLNLLITLMTLLVFTEVVARFFFNTGFLWIQELTLTLCGWFVLFGMSY 60

Query: 61  GVKVGAHIGVDAFVKKLPAQGRKYTAILAVAICLIYCGMFLVGSWDYLAKMYQIGVPMED 120
           GVKVGAHIGVDAFVK LP + +K T+++   ICL YCG+FL GSW+YL++MYQIGVPMED
Sbjct: 61  GVKVGAHIGVDAFVKNLPPKAKKITSLVTALICLAYCGLFLKGSWEYLSQMYQIGVPMED 120

Query: 121 IDLPHFLIGGLDGDFAWEYLRIDVEEPAVPLWTSQSILLIGFILLTWRFLQLALAIITNK 180
           I  P FL+  LD DFAW  L+IDVE+ AVP+W SQSILLIGF +LTWRFL+L +AI+ N+
Sbjct: 121 IHFPKFLLNSLDPDFAWNTLKIDVEDGAVPIWLSQSILLIGFSMLTWRFLELFIAILRNQ 180

Query: 181 TDGFAFADEAKESMHLIDQEAQADDKQPGDKK 212
             GF FADEAKESMHLID+ AQ   ++  +K+
Sbjct: 181 VSGFQFADEAKESMHLIDEAAQHAQQETDNKE 212


Lambda     K      H
   0.329    0.144    0.453 

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: 234
Number of extensions: 8
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: 212
Length of database: 214
Length adjustment: 22
Effective length of query: 190
Effective length of database: 192
Effective search space:    36480
Effective search space used:    36480
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 (21.8 bits)
S2: 45 (21.9 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