GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AZOBR_RS08245 in Magnetospirillum magneticum AMB-1

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_083763604.1 AMB_RS09125 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>lcl|NCBI__GCF_000009985.1:WP_083763604.1 AMB_RS09125 ABC
           transporter ATP-binding protein
          Length = 257

 Score =  360 bits (923), Expect = e-104
 Identities = 186/256 (72%), Positives = 209/256 (81%), Gaps = 1/256 (0%)

Query: 19  MRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLRHADGKEF 78
           MRFGGL AVND+SFSA   EITA+IGPNGAGKTTLFNCITGFY P VGR+TL H  G   
Sbjct: 1   MRFGGLFAVNDLSFSAAPKEITAVIGPNGAGKTTLFNCITGFYKPQVGRMTLDHPSGP-M 59

Query: 79  LLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAGLLGLPSY 138
           LLER+  + IS KA VARTFQNIRLF  MSVLENLIVAQH  L+RAS FS+AGLLGL  Y
Sbjct: 60  LLERLDDFAISAKAGVARTFQNIRLFARMSVLENLIVAQHTTLMRASAFSLAGLLGLSRY 119

Query: 139 TRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLCLDEPAAG 198
            R E  AV+ A++WLD+V L   AD EAG+LPYG QRRLEIARAMCT P++LCLDEPAAG
Sbjct: 120 ARAEARAVERARHWLDKVGLTSLADEEAGSLPYGHQRRLEIARAMCTGPLLLCLDEPAAG 179

Query: 199 LNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISDGDPAFVKN 258
           LNPRES EL  LL  IRDE+ IG+LLIEHDMSVVM ISDH+VVLDYG+KI++G PA +K 
Sbjct: 180 LNPRESAELNRLLLDIRDENGIGLLLIEHDMSVVMEISDHIVVLDYGKKIAEGAPAAIKA 239

Query: 259 DPAVIRAYLGEEEDEE 274
           DPAVIRAYLGE ++EE
Sbjct: 240 DPAVIRAYLGEPDEEE 255


Lambda     K      H
   0.319    0.137    0.397 

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: 261
Number of extensions: 5
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: 294
Length of database: 257
Length adjustment: 25
Effective length of query: 269
Effective length of database: 232
Effective search space:    62408
Effective search space used:    62408
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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