GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapQ in Herbaspirillum seropedicae SmR1

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 HSERO_RS19340 HSERO_RS19340 amino acid ABC transporter permease

Query= TCDB::Q52813
         (400 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS19340 HSERO_RS19340 amino acid
           ABC transporter permease
          Length = 216

 Score = 86.7 bits (213), Expect = 6e-22
 Identities = 69/211 (32%), Positives = 97/211 (45%), Gaps = 24/211 (11%)

Query: 195 IALVIAIVASIIIARW-----AHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTF 249
           +A V   VA  +IA W     A  R  A+G         I ++ G+PLLV +   F   F
Sbjct: 25  VAFVFGGVAGFVIALWRVSPNAVLRGIASGY--------IQVVQGIPLLVIL---FVAYF 73

Query: 250 DVPVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLH 309
            + +AG F LT     G  F       + Y A+F+ EI RG I+ VPK Q EA+  LG +
Sbjct: 74  GLAIAG-FKLTPLVAAGISF-------AIYCAAFLGEIWRGCIQAVPKTQWEASECLGFN 125

Query: 310 PSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEI 369
                  V++PQA++I  PP     + + KN+SLA  IGF DL   G  I N + Q   +
Sbjct: 126 RFEQLTKVILPQAVKIATPPTVGFMVQIVKNTSLASVIGFVDLSRAGQIINNSTFQPFTV 185

Query: 370 VCIWGIVYLSLSILTSLFMNWFNAKMALVER 400
                ++Y  L    S     F  K+ +  R
Sbjct: 186 FGCVALIYFCLCFPLSALSKHFERKLNVSHR 216



 Score = 40.8 bits (94), Expect = 4e-08
 Identities = 21/84 (25%), Positives = 46/84 (54%), Gaps = 2/84 (2%)

Query: 92  LLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLVIFFW 151
           LL   + T+++++       + GF+I + R+S N ++  + + Y++V + IP L+++F  
Sbjct: 12  LLQAAVWTVVLSLVAFVFGGVAGFVIALWRVSPNAVLRGIASGYIQVVQGIPLLVILFVA 71

Query: 152 YLG--VLSVLPQPRESVGLPFSMY 173
           Y G  +      P  + G+ F++Y
Sbjct: 72  YFGLAIAGFKLTPLVAAGISFAIY 95


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: 247
Number of extensions: 14
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: 216
Length adjustment: 26
Effective length of query: 374
Effective length of database: 190
Effective search space:    71060
Effective search space used:    71060
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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