GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Mesorhizobium ciceri WSM1271

Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate YP_004139338.1 Mesci_0115 polar amino acid ABC transporter inner membrane subunit

Query= uniprot:Q31RN9
         (396 letters)



>NCBI__GCF_000185905.1:YP_004139338.1
          Length = 224

 Score =  115 bits (289), Expect = 9e-31
 Identities = 73/210 (34%), Positives = 118/210 (56%), Gaps = 13/210 (6%)

Query: 190 GLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVTILFFGQVM 249
           G L TL   ++S+   +P+G+ ++L R  +   +RWL+V Y ++FR LP++ +L      
Sbjct: 23  GFLNTLLLGILSIGIGIPIGLGISLVRLYAPKPLRWLAVGYTDIFRALPVLVVLILIYYA 82

Query: 250 VPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALGLNLFQTYR 309
           +P +     R+     A+      +SAY AE  R G+++IP+GQFEA+ ALGL    T R
Sbjct: 83  LPFL---GIRLSSWASAVTAFAFIMSAYSAEVFRSGIESIPRGQFEASQALGLPFLLTLR 139

Query: 310 FIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELL---GISRSILANPAYLGRYAEV 366
            +VLPQA+R+ IP +    +++ +DT+L S V L ELL     ++S+ ANP+ L   A V
Sbjct: 140 KVVLPQAIRVVIPPMTSNCVSMFKDTSLASTVALPELLKEATNAQSLYANPSPLIGAALV 199

Query: 367 YLFLGVLYWLCCYGLAQLSRRLEQRLTPQR 396
           YL   +  W     + +L   LE+R   ++
Sbjct: 200 YL---IFLW----PMVRLVSLLEERFKTEK 222


Lambda     K      H
   0.329    0.142    0.471 

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: 224
Number of extensions: 6
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: 396
Length of database: 224
Length adjustment: 26
Effective length of query: 370
Effective length of database: 198
Effective search space:    73260
Effective search space used:    73260
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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