GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Desulfovibrio vulgaris Hildenborough

Align AapM, 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 206399 DVU0967 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family

Query= TCDB::Q52814
         (384 letters)



>MicrobesOnline__882:206399
          Length = 337

 Score =  116 bits (291), Expect = 8e-31
 Identities = 65/209 (31%), Positives = 119/209 (56%), Gaps = 11/209 (5%)

Query: 174 GLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFM---- 229
           GL +TL +S + I + + +G++  L R S  P +R L +T+IE+IRG PL+  +F+    
Sbjct: 130 GLWITLEVSMLAIIIGIVLGVVTGLARISVNPALRWLAITYIEIIRGSPLLVQVFLWYFV 189

Query: 230 -ASVMLPLFLPTGWN-VDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLG 287
             +++  LF   G + +  L   ++ ++IFT AY+AE++R G+Q++ +GQ E A SLG+ 
Sbjct: 190 VGTLLNALFEKVGLSAIPPLWYGVMALAIFTGAYVAEIVRAGIQSVHRGQMEAARSLGMS 249

Query: 288 YWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAV 347
           Y Q  R +I+PQA + ++P +   FI   KD+SL+ +I + +L    +   +     +++
Sbjct: 250 YAQSMRKVILPQAFRRIMPPLAGQFISLVKDSSLLGVIAVRELTKATREVVT-----TSL 304

Query: 348 TPITGLIFAGFIFWLFCFGMSRYSGFMER 376
            P    I    ++ +  F +S    ++ER
Sbjct: 305 QPFELWIVCALLYLVLTFTLSLCVQYLER 333


Lambda     K      H
   0.330    0.145    0.469 

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: 350
Number of extensions: 17
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: 384
Length of database: 337
Length adjustment: 29
Effective length of query: 355
Effective length of database: 308
Effective search space:   109340
Effective search space used:   109340
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: 49 (23.5 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:

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