GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Brucella inopinata BO1

Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate WP_008511689.1 BIBO1_RS19985 amino acid ABC transporter permease

Query= TCDB::Q8YPM7
         (381 letters)



>NCBI__GCF_000182725.1:WP_008511689.1
          Length = 323

 Score =  126 bits (316), Expect = 1e-33
 Identities = 92/283 (32%), Positives = 146/283 (51%), Gaps = 31/283 (10%)

Query: 99  LFAFIVGLLLILFTLDLSSRLWLLLTAVLLIPGFLLGSRLTNLVAPWLSLIWLLSFPIIL 158
           L AF + L+L L         W LL  +         SR   +VA W  L  LL      
Sbjct: 60  LSAFSISLILFLN--------WKLLKRL---------SRNQQVVAVWTELFVLLMIFFYS 102

Query: 159 WLIGGGFGLRPVSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYI 218
           + +   F  R +S  +  G + TL ++AISI ++  I ++ A+ + S   V+   S  Y 
Sbjct: 103 FDLSFSFIARKISFLITQGTVTTLYISAISIAIATIIALIGAIAKLSQNGVIYGLSTFYT 162

Query: 219 EIVRGVPLIGILFLAQVMLPLFFAADVRLDRVLRAI-AGLVLFS---AAYMAENVRGGLQ 274
            + RG+PL+  +++  + LP       ++  V+ AI AG++  S    AYM E  R G++
Sbjct: 163 SLFRGLPLLMQIYIIYLGLP-------QIGYVIGAIPAGILALSLCYGAYMTEIFRAGIE 215

Query: 275 AVSRGQVEAAKALGLNTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELT 334
           ++  GQ EAA ALGL +   + L++LPQA+R +IP    QFI + KD+SL+S++G+ EL 
Sbjct: 216 SIPHGQKEAATALGLGSAQTMWLVILPQAMRIIIPPTGNQFIAMLKDSSLVSVIGVWELM 275

Query: 335 GIARSILAQPQFIGRYAEVYLFIGLIYWLFCYSMSLASRRLER 377
            +AR+   Q Q   R+ E+ +   +IYW+   S      R+ER
Sbjct: 276 YVART---QGQTEFRHIEMLITASMIYWILSISFEFIQSRIER 315


Lambda     K      H
   0.332    0.145    0.452 

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: 373
Number of extensions: 16
Number of successful extensions: 3
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: 381
Length of database: 323
Length adjustment: 29
Effective length of query: 352
Effective length of database: 294
Effective search space:   103488
Effective search space used:   103488
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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