GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0549 in Acidovorax sp. GW101-3H11

Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate Ac3H11_794 Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3)

Query= reanno::Dino:3607127
         (272 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_794
          Length = 270

 Score =  160 bits (406), Expect = 2e-44
 Identities = 86/258 (33%), Positives = 127/258 (49%)

Query: 14  LVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREALFEDGVLRTLINSLI 73
           L+  +   + P YWMV  S KT    L     +    T  NY+    ++      INSLI
Sbjct: 13  LIAYLLFALLPIYWMVNMSFKTNAEILSTFSFFPQHFTWDNYKTIFTDESWYSGYINSLI 72

Query: 74  IAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLIARNLGLL 133
                  + L + +PAA+A +R+ F G K ++FW +TNRM  P V  LPFF +   +GL+
Sbjct: 73  YVSINMVITLTVALPAAYAFSRYSFLGDKHVFFWLLTNRMTPPAVFLLPFFQLYTTVGLM 132

Query: 134 DKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPLAMPGV 193
           D HI + L +L F++P+ +WI+     GIP ++DE A ++G S       I LPL   GV
Sbjct: 133 DTHIAVALAHLLFSVPLAVWILEGFMSGIPREIDETAYIDGYSFPRFFMTIFLPLIKAGV 192

Query: 194 AVSAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEGYNLPYGKIMATSTLIVIPVLI 253
            V+A F F+FSW EL+    LT   AK   A     +    + +  + A   L ++P  I
Sbjct: 193 GVAAFFCFMFSWVELLLARTLTSVNAKPIVATMTRTVSASGMDWATLAAAGVLTIVPGAI 252

Query: 254 FALIASKQLVRGLTMGAV 271
                   + +G  MG V
Sbjct: 253 VIWFVRHYIAKGFAMGRV 270


Lambda     K      H
   0.331    0.143    0.431 

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: 249
Number of extensions: 13
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: 272
Length of database: 270
Length adjustment: 25
Effective length of query: 247
Effective length of database: 245
Effective search space:    60515
Effective search space used:    60515
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 (21.9 bits)
S2: 47 (22.7 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