GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG' in Herbaspirillum seropedicae SmR1

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate HSERO_RS22745 HSERO_RS22745 sugar ABC transporter permease

Query= uniprot:A8LLL4
         (385 letters)



>FitnessBrowser__HerbieS:HSERO_RS22745
          Length = 300

 Score =  113 bits (283), Expect = 6e-30
 Identities = 73/236 (30%), Positives = 127/236 (53%), Gaps = 10/236 (4%)

Query: 152 TPPEFTFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPG- 210
           T    TFA ++ +L   +        F N+L VT+ A  + +L  A AA+AL    F G 
Sbjct: 73  TAETLTFAGFQKVLAGTH----FLLYFGNSLAVTVAALFLIVLFGAMAAWALTEYRFFGN 128

Query: 211 RALLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMV 270
           RAL   + +G+++ P++L  + +L L  A+ +        L +T  G+PLA+ +L  +M 
Sbjct: 129 RALNFFIAIGIMI-PIRLGTVSILQLVVALDLINTRTALVLVYTAQGLPLAVMILSEFMR 187

Query: 271 GLPRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATG 330
            +P ++ + A+ DG  +  IF +++LPL  PA+A+ A+F  +  WNDL      LI A G
Sbjct: 188 QIPGELKDAARCDGVGELSIFFRVILPLLRPAIATVAVFTMIPAWNDLWFP---LILAPG 244

Query: 331 Q-TTVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385
           + T  +T  + + +G    +W  +  A  +++   LL++ +  R L+RGL +G+VK
Sbjct: 245 EDTRTVTLGVQQFIGQYATDWNSVLAALSMAVIPVLLLYMAFSRQLIRGLTSGAVK 300


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: 248
Number of extensions: 11
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: 300
Length adjustment: 28
Effective length of query: 357
Effective length of database: 272
Effective search space:    97104
Effective search space used:    97104
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: 49 (23.5 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