GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Caldicellulosiruptor hydrothermalis 108

Align AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate WP_013402767.1 CALHY_RS04220 amino acid ABC transporter permease

Query= TCDB::Q52813
         (400 letters)



>NCBI__GCF_000166355.1:WP_013402767.1
          Length = 220

 Score = 85.1 bits (209), Expect = 2e-21
 Identities = 65/213 (30%), Positives = 104/213 (48%), Gaps = 22/213 (10%)

Query: 191 IAVGIALVIAIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLV---FVVSGFPL 247
           IAV I LV  +VA++       K +         VW    L  G PLL+   F+  G P 
Sbjct: 26  IAVTIGLVFGLVAALFRIS---KIKVLNYIGSFYVW----LFRGTPLLLQIFFIYYGLPK 78

Query: 248 TFDVPVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALG 307
              VP          ++  P F++  +AL   + ++ AEI+R  I  + KGQ EAA ALG
Sbjct: 79  I--VP----------ALTLPAFLAGAIALIINSGAYTAEIIRAAILSIDKGQYEAAKALG 126

Query: 308 LHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAI 367
           +      R V+VPQ  + +IPP+ ++++ L K+SSL   IG  +L+       + +G+  
Sbjct: 127 MTYLQTMRYVIVPQTYKRLIPPIGNEFIALLKDSSLVSTIGMVELMRAAQLKASATGRDA 186

Query: 368 EIVCIWGIVYLSLSILTSLFMNWFNAKMALVER 400
           EI     ++YL+L+ + S   NW   ++   E+
Sbjct: 187 EIYIAALVIYLALTTVFSTIFNWLEKRLGKYEQ 219



 Score = 37.0 bits (84), Expect = 5e-07
 Identities = 20/73 (27%), Positives = 37/73 (50%)

Query: 88  YARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLV 147
           Y   LL   + T+ +    +    + G +  + R+S+  ++  + + YV +FR  P LL 
Sbjct: 9   YFPVLLKASVVTIELTAIAVTIGLVFGLVAALFRISKIKVLNYIGSFYVWLFRGTPLLLQ 68

Query: 148 IFFWYLGVLSVLP 160
           IFF Y G+  ++P
Sbjct: 69  IFFIYYGLPKIVP 81


Lambda     K      H
   0.327    0.141    0.432 

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: 208
Number of extensions: 11
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 400
Length of database: 220
Length adjustment: 26
Effective length of query: 374
Effective length of database: 194
Effective search space:    72556
Effective search space used:    72556
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 (21.7 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