GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araWsh in Acidovorax sp. GW101-3H11

Align Inner-membrane translocator (characterized, see rationale)
to candidate Ac3H11_606 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)

Query= uniprot:A0KWY6
         (405 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_606
          Length = 337

 Score =  303 bits (776), Expect = 5e-87
 Identities = 162/323 (50%), Positives = 222/323 (68%), Gaps = 6/323 (1%)

Query: 61  RYLWPLLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIAT 120
           R  WPL+ L++LL+ N   +SSF +I ++D  LYGSLIDILNR+AP+ L+S+GM+LVIAT
Sbjct: 5   RLAWPLITLALLLVVNTVFNSSFLHIEWRDGHLYGSLIDILNRAAPLVLVSLGMTLVIAT 64

Query: 121 GGIDLSVGAVMAIAGAVCANLL------LVPDISLVTVIAAGLIVGLLAGCINGGLVSFL 174
            GID+SVGA +AIA AV A ++            L   I   + V LL G  NG LV+ +
Sbjct: 65  RGIDISVGATVAIAAAVAAWMIGGSVSGTESRFPLPVAILGAIGVALLCGLWNGVLVAKV 124

Query: 175 GIQPIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFS 234
           G+QPI+ATL+LMVAGRG+AQLI  GQIIT  +  +  +G G   GLP  V++V  +    
Sbjct: 125 GMQPIIATLILMVAGRGIAQLITDGQIITIYYTPYFFLGGGYLAGLPFSVFVVAAVFVAL 184

Query: 235 QLLLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSD 294
            L + +TALGLFI+AVG N  A+R  G+    + + AY   G+CA +AG++ +++++ +D
Sbjct: 185 YLAITRTALGLFIQAVGINPTAARVAGVQAGRLIVAAYVFCGVCAGIAGLLISSNVKSAD 244

Query: 295 ANNAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLI 354
            NNAG  LELDA+LAV +GG ALTGGRFSL+ SV+GALIIQTL   I   G+P + NL++
Sbjct: 245 GNNAGQLLELDAILAVTLGGTALTGGRFSLVGSVIGALIIQTLTYAIYSLGVPPEINLVV 304

Query: 355 KAIVILTVLLLQSAKFRRQLSAL 377
           KA+V+  V+LLQS +FR Q+ AL
Sbjct: 305 KAVVVFIVMLLQSPEFRAQVGAL 327


Lambda     K      H
   0.323    0.136    0.379 

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: 370
Number of extensions: 24
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: 405
Length of database: 337
Length adjustment: 30
Effective length of query: 375
Effective length of database: 307
Effective search space:   115125
Effective search space used:   115125
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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