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_043745616.1 AMB_RS21885 ABC transporter

Query= uniprot:Q31RN8
         (261 letters)



>NCBI__GCF_000009985.1:WP_043745616.1
          Length = 229

 Score =  128 bits (322), Expect = 9e-35
 Identities = 81/205 (39%), Positives = 121/205 (59%), Gaps = 7/205 (3%)

Query: 34  QFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRLSH-DRRD 92
           +   L G+ L V  GE + ++GPSGSGKST L  +  LE    G++ + G      D   
Sbjct: 27  EVNVLDGIDLQVASGETLGVVGPSGSGKSTLLMVMAGLERPTSGKVAVAGQDFGPMDEDG 86

Query: 93  IATIRQE-VGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVRIAEQA 151
           +A  R++ +G+VFQ F+L P +T L+N+ + P+++     A     A++ L RV +A + 
Sbjct: 87  LARFRRDSIGIVFQSFHLIPTMTALENVAV-PLELAGH--ADPFGAAQEELGRVGLAHRL 143

Query: 152 DKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRDL-ASEGMTM 210
             YPGQLSGG+QQRVA+ARA   +P++LL DEPT  LD    R V+D++ DL A  G  +
Sbjct: 144 SHYPGQLSGGEQQRVALARAFVPRPKLLLADEPTGNLDGATGRAVMDLLFDLNARFGTAL 203

Query: 211 LVATHEVGFAREVADRVVLMADGQI 235
           ++ TH+   A     RVV + DG+I
Sbjct: 204 VLVTHDDSLAAR-CTRVVRVEDGKI 227


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: 138
Number of extensions: 7
Number of successful extensions: 3
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: 229
Length adjustment: 24
Effective length of query: 237
Effective length of database: 205
Effective search space:    48585
Effective search space used:    48585
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