GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Brucella inopinata BO1

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate WP_008511689.1 BIBO1_RS19985 amino acid ABC transporter permease

Query= reanno::Smeli:SMc02120
         (384 letters)



>NCBI__GCF_000182725.1:WP_008511689.1
          Length = 323

 Score =  115 bits (289), Expect = 1e-30
 Identities = 66/207 (31%), Positives = 111/207 (53%), Gaps = 8/207 (3%)

Query: 175 GLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVM 234
           G + TL +S + IA++  + ++ A+ + S   VI  L T +  + RG+PL+  +++  + 
Sbjct: 121 GTVTTLYISAISIAIATIIALIGAIAKLSQNGVIYGLSTFYTSLFRGLPLLMQIYIIYLG 180

Query: 235 LPLFLPQGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMG 294
           LP     G         ++ +SL   AYM E+ R G+++IP GQ E A +LGL   Q M 
Sbjct: 181 LPQI---GYVIGAIPAGILALSLCYGAYMTEIFRAGIESIPHGQKEAATALGLGSAQTMW 237

Query: 295 FIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFSDTNWATAVTPLTGL 354
            ++LPQA++++IP   N FI + KD+SLVS+IG+++L+ + R     T   T    +  L
Sbjct: 238 LVILPQAMRIIIPPTGNQFIAMLKDSSLVSVIGVWELMYVAR-----TQGQTEFRHIEML 292

Query: 355 IFAGFVFWLFCFGMSRYSGFMERLLDR 381
           I A  ++W+           +ER   R
Sbjct: 293 ITASMIYWILSISFEFIQSRIERYYAR 319


Lambda     K      H
   0.329    0.144    0.454 

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: 320
Number of extensions: 16
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: 384
Length of database: 323
Length adjustment: 29
Effective length of query: 355
Effective length of database: 294
Effective search space:   104370
Effective search space used:   104370
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: 49 (23.5 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