GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_17600 in Desulfovibrio vulgaris Hildenborough

Align ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale)
to candidate 207827 DVU2340 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family

Query= uniprot:A0A1N7U128
         (237 letters)



>lcl|MicrobesOnline__882:207827 DVU2340 amino acid ABC transporter,
           permease protein, His/Glu/Gln/Arg/opine family
          Length = 230

 Score =  103 bits (258), Expect = 2e-27
 Identities = 70/229 (30%), Positives = 114/229 (49%), Gaps = 11/229 (4%)

Query: 8   YGLAYLFSDGAGLSGVAMTLWLFIISVVLGFFLSIPLALARVSEHVWLRWPVEVYTYLFR 67
           Y L   + DG  L G+AM++ L I  +   F+L +   L R+SE  W+R P  VY  + R
Sbjct: 12  YLLVGSYPDGP-LGGMAMSILLAIGGIFGAFWLGLAFGLMRLSEKWWVRAPAIVYVEVIR 70

Query: 68  GTPLYIQLLICYTGLYSLEIVQDNALLNQFFRNALNCTLLAFVLNTCAYTVEIFAGAIRN 127
           G PL   L++ +   +   I   + L            L+AF++ T AY  EI    +  
Sbjct: 71  GIPL---LMLIFWFYFLAPIALGHTLPEA------ESALIAFIVFTGAYIAEIVRAGVLA 121

Query: 128 IPHGEIEAARAYGLHGWRLNLFVVVPAALRRALPAYSNEMILMLHATSLAFTATVADILK 187
           +P G++EAAR  GL   +  LFV++P ALR  +P++ N+ + +   TSLA+   V+++ +
Sbjct: 122 LPAGQMEAARGTGLSKTQAMLFVILPQALRNMIPSFVNQFVSLTKDTSLAYIIGVSELTR 181

Query: 188 VARDANAETFLT-FQAFGIAALLYMLLSFALVGLFRLAERRWMRFLVPT 235
            A   N  T     + F   AL+Y ++ + L    R  E++  R+   T
Sbjct: 182 TATQVNNRTLTAPTEIFLTIALMYFVICWVLTATSRRLEKQMARYQART 230


Lambda     K      H
   0.332    0.143    0.443 

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: 169
Number of extensions: 11
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: 237
Length of database: 230
Length adjustment: 23
Effective length of query: 214
Effective length of database: 207
Effective search space:    44298
Effective search space used:    44298
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 (22.0 bits)
S2: 46 (22.3 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