GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Pf6N2E2_5403 in Desulfovibrio vulgaris Hildenborough

Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate 207828 DVU2341 amino acid ABC transproter, permease protein, His/Glu/Gln/Arg/opine family

Query= reanno::pseudo6_N2E2:Pf6N2E2_5403
         (375 letters)



>lcl|MicrobesOnline__882:207828 DVU2341 amino acid ABC transproter,
           permease protein, His/Glu/Gln/Arg/opine family
          Length = 233

 Score =  105 bits (262), Expect = 1e-27
 Identities = 59/126 (46%), Positives = 80/126 (63%), Gaps = 1/126 (0%)

Query: 242 ELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVII 301
           E  A  ++LTVYTAAFIAE +RSGI S+   Q EA+R+ GL     +  V++PQA R+I+
Sbjct: 100 EFAAGVISLTVYTAAFIAEEIRSGIFSIPRTQLEASRACGLSFMQAMSYVVLPQAFRIIV 159

Query: 302 PPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISL 361
           PPL SQ LNL KNSSL   IG  E+ +  A  + + T    E   ++  +YL IS+ +SL
Sbjct: 160 PPLISQALNLFKNSSLCMTIGVMEL-TYMARQIESYTFHGFEAFTVSTLIYLCISLMVSL 218

Query: 362 LMNWYN 367
           L+N YN
Sbjct: 219 LINLYN 224



 Score = 47.8 bits (112), Expect = 3e-10
 Identities = 24/66 (36%), Positives = 37/66 (56%)

Query: 69  GLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQILFWYFA 128
           G++ T  ++ + ++LA +LG +I V RLS        +  + E FRN P L+QI FWYF 
Sbjct: 22  GVITTCQLSGLSLVLAMLLGTLIAVMRLSGVRPFVWFSVAFTEFFRNTPLLVQIFFWYFG 81

Query: 129 VFLSMP 134
               +P
Sbjct: 82  SDAVLP 87


Lambda     K      H
   0.328    0.141    0.430 

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: 192
Number of extensions: 8
Number of successful extensions: 4
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: 375
Length of database: 233
Length adjustment: 26
Effective length of query: 349
Effective length of database: 207
Effective search space:    72243
Effective search space used:    72243
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: 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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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