GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08240 in Frankia alni ACN14a

Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_041938756.1 FRAAL_RS03130 branched-chain amino acid ABC transporter permease

Query= uniprot:G8ALI9
         (505 letters)



>NCBI__GCF_000058485.1:WP_041938756.1
          Length = 515

 Score =  213 bits (543), Expect = 1e-59
 Identities = 135/359 (37%), Positives = 198/359 (55%), Gaps = 36/359 (10%)

Query: 151 LGPIAVVVALAFPF---TPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFY 207
           L  + + VA+  P    T      + DIGI    Y +L  GLN+VVG AGLLDLGY+AF+
Sbjct: 178 LNLVLLAVAILAPLVVSTAAQQSMVNDIGI----YALLALGLNVVVGYAGLLDLGYIAFF 233

Query: 208 AVGAYSYALLAHY--------FGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVT 259
           A+GAY+ A             F  + +   P+A  LAA++GV+LG P LRLRGDY AIVT
Sbjct: 234 AIGAYATAYFTSQTAMPWHAPFVLNPFFVFPIALVLAALAGVILGAPTLRLRGDYLAIVT 293

Query: 260 LGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPL 319
           LGFGEII ++  N    T G  G  G+P  S                   ++ G+++   
Sbjct: 294 LGFGEIIHLVANNADGITNGARGAFGVPHLSI------------------DLLGIDYKWG 335

Query: 320 HRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAI 379
              +  YYL+L + + V +   R+ +  +GR+W A+RED+IA  + G+    MKL AFAI
Sbjct: 336 IDPLPYYYLLLAIVIGVMIAFGRLERSRIGRSWAAIREDEIAAEATGVATLRMKLLAFAI 395

Query: 380 AAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEA 439
            A   GFAG  FA++Q F +P+SF+   S  ++A+V+ GGMGS++GVVV A ++ GL   
Sbjct: 396 GASVSGFAGVLFASKQ-FFNPQSFSLQASFFVVAVVIFGGMGSRLGVVVGAVVLQGLAFY 454

Query: 440 FRELAD--YRMLAFGMGMVLIMLWRPRGLLAHRDPTILLHGRPKGGAGGPAAGSAAAGG 496
            R+      R + FG  +V++M++RP+GL+  R     +    +G     + G+A  GG
Sbjct: 455 LRDKVQPADRYIYFGAVIVIMMIFRPQGLVPSRRRRREIELAEEGIGAADSLGAAPTGG 513


Lambda     K      H
   0.329    0.144    0.438 

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: 706
Number of extensions: 46
Number of successful extensions: 5
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: 505
Length of database: 515
Length adjustment: 34
Effective length of query: 471
Effective length of database: 481
Effective search space:   226551
Effective search space used:   226551
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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