GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Dinoroseobacter shibae DFL-12

Align ATPase (characterized, see rationale)
to candidate 3607646 Dshi_1055 ABC transporter related (RefSeq)

Query= uniprot:Q31RN8
         (261 letters)



>FitnessBrowser__Dino:3607646
          Length = 366

 Score =  150 bits (379), Expect = 4e-41
 Identities = 89/228 (39%), Positives = 135/228 (59%), Gaps = 7/228 (3%)

Query: 22  IYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWI 81
           +  +G+ K YG   +AL  V LT+  GE  V++GPSG GK+T LRT+        G++ +
Sbjct: 9   VEVKGLSKHYG-PVKALRQVDLTIAAGEYFVLLGPSGGGKTTLLRTIGGFHRPTEGQVLL 67

Query: 82  EGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQL 141
            G  +SH   D    ++   MVFQ + LFPH+TVLQN+    ++V     A A+  A  +
Sbjct: 68  HGRDMSHLPPD----KRPTTMVFQAYALFPHMTVLQNVSYG-LKVAGMDKATAQEKAAAM 122

Query: 142 LERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMR 201
           ++ V +A  A++ P +LSGGQQQRV +ARAL +   ILL DEP +ALD ++ +++   ++
Sbjct: 123 MDVVGLAGFAERKPHELSGGQQQRVQLARALVLDRDILLLDEPLAALDAQLRKDMCLELK 182

Query: 202 DLASE-GMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAP 248
            L  + G+T +  TH    A  VADR+ L+ADGQ+VE+      + AP
Sbjct: 183 HLQEKVGITFIHVTHNQEEAMTVADRIALVADGQLVEQGAARDIYRAP 230


Lambda     K      H
   0.321    0.134    0.387 

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: 244
Number of extensions: 14
Number of successful extensions: 4
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: 261
Length of database: 366
Length adjustment: 27
Effective length of query: 234
Effective length of database: 339
Effective search space:    79326
Effective search space used:    79326
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 (21.9 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:

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