GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SMc02869 in Dyella japonica UNC79MFTsu3.2

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate N515DRAFT_1821 N515DRAFT_1821 putative ABC transport system ATP-binding protein

Query= reanno::Smeli:SMc02869
         (352 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1821 N515DRAFT_1821 putative
           ABC transport system ATP-binding protein
          Length = 238

 Score =  127 bits (320), Expect = 2e-34
 Identities = 82/215 (38%), Positives = 117/215 (54%), Gaps = 10/215 (4%)

Query: 35  LKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGL-EDATSGSVQIDGVEVGHVAPAKRG- 92
           L+  ++DVK+GEFV   GPSG GK+T L TIAGL E  T G   +DGVEV ++    R  
Sbjct: 21  LRDFNIDVKEGEFVAVTGPSGSGKTTFL-TIAGLLETFTGGEYHLDGVEVSNLNDNARSK 79

Query: 93  -----IAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLSLEPYLARRP 147
                I  +FQ++ L P L V DN+ + L+  G+   E ++++  A   + L       P
Sbjct: 80  IRNEKIGFIFQAFNLIPDLNVYDNVEVPLRYRGMKALERKQRIMDALERVGLASRAKHYP 139

Query: 148 AELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRSLKATMIYVT 207
           AELSGGQ+QRVAI RA+   P+L L DEP  NLD  +       +  +HR   AT++ VT
Sbjct: 140 AELSGGQQQRVAIARALAGSPRLLLADEPTGNLDTQMARGVMELLEEIHRE-GATIVMVT 198

Query: 208 HDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPA 242
           HD  E  T A + V +  G++  +      + + A
Sbjct: 199 HDP-ELATRAQRNVHVIDGQVVDLAEDPRFHQQQA 232


Lambda     K      H
   0.320    0.137    0.393 

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: 192
Number of extensions: 7
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: 352
Length of database: 238
Length adjustment: 26
Effective length of query: 326
Effective length of database: 212
Effective search space:    69112
Effective search space used:    69112
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 (21.8 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 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