GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Magnetospirillum magneticum AMB-1

Align ATPase (characterized, see rationale)
to candidate WP_011385145.1 AMB_RS13910 ABC transporter ATP-binding protein

Query= uniprot:Q31RN8
         (261 letters)



>NCBI__GCF_000009985.1:WP_011385145.1
          Length = 224

 Score =  134 bits (336), Expect = 2e-36
 Identities = 83/199 (41%), Positives = 116/199 (58%), Gaps = 4/199 (2%)

Query: 41  VSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRLSHDRRD-IATIR-Q 98
           + LTV RGE V + GPSGSGKS+ L  L  L+    G +W++G   +    D +A +R  
Sbjct: 26  IDLTVGRGEFVAVTGPSGSGKSSLLYLLGLLDVPTGGSVWLQGGNTAGLPPDAMAELRLA 85

Query: 99  EVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVRIAEQADKYPGQL 158
            +G VFQ   L P  T   N+ +   ++     +QA   A +LL+ + +A+   KYP QL
Sbjct: 86  SIGFVFQFHFLLPEFTCQSNVEIPIRRLGALSDSQARIRAAELLDSLELADHRRKYPDQL 145

Query: 159 SGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRDLA-SEGMTMLVATHEV 217
           SGGQ+QRVAIARALA  P ++L DEPT  LD      V ++ RDLA  +  T++V TH+ 
Sbjct: 146 SGGQRQRVAIARALANDPPLILADEPTGNLDTRTAHLVFELFRDLAHRQNRTVIVVTHDA 205

Query: 218 GFAREVADRVVLMADGQIV 236
             A + ADR V + DG+IV
Sbjct: 206 ELA-QTADRRVHLVDGRIV 223


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: 156
Number of extensions: 8
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: 261
Length of database: 224
Length adjustment: 23
Effective length of query: 238
Effective length of database: 201
Effective search space:    47838
Effective search space used:    47838
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: 46 (22.3 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