GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG in Dinoroseobacter shibae DFL-12

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate 3607127 Dshi_0549 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= uniprot:A8LLL4
         (385 letters)



>FitnessBrowser__Dino:3607127
          Length = 272

 Score =  110 bits (274), Expect = 6e-29
 Identities = 75/244 (30%), Positives = 125/244 (51%), Gaps = 15/244 (6%)

Query: 148 VTATTPP----EFTFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYAL 203
           V    PP    E T +NY   L +    +G+ R   N+L + I  T + +++   AA+AL
Sbjct: 38  VALEAPPVWIFEPTLSNYREALFE----DGVLRTLINSLIIAISTTFLALVLGVPAAFAL 93

Query: 204 AWMEFPGRA-LLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAI 262
           A  EF G+  L    I   ++ P+ LAL P   +   +G+   ++   L +  F +P+ I
Sbjct: 94  ARFEFRGKKDLWFWFITNRMISPIVLAL-PFFLIARNLGLLDKHITLILIYLTFNLPIVI 152

Query: 263 YLLRNYMVGLPRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAK 322
           +++ +   G+P D+ E A+++GA+ F I  KI LPL+ P +A  AIF F+++WN+L+   
Sbjct: 153 WIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPLAMPGVAVSAIFSFIFSWNELMFGL 212

Query: 323 VFLIDATGQTTVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVF-FSMQRFLVRGLLA 381
           +           M    +E      G  +I+AT+    I +P+L+F     + LVRGL  
Sbjct: 213 ILTRSEAKTAPAMAVSFMEGYNLPYG--KIMATSTL--IVIPVLIFALIASKQLVRGLTM 268

Query: 382 GSVK 385
           G+VK
Sbjct: 269 GAVK 272


Lambda     K      H
   0.323    0.138    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: 214
Number of extensions: 9
Number of successful extensions: 2
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: 385
Length of database: 272
Length adjustment: 28
Effective length of query: 357
Effective length of database: 244
Effective search space:    87108
Effective search space used:    87108
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 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