GapMind for catabolism of small carbon sources

 

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

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_011384429.1 AMB_RS10230 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>NCBI__GCF_000009985.1:WP_011384429.1
          Length = 234

 Score =  221 bits (563), Expect = 1e-62
 Identities = 117/233 (50%), Positives = 164/233 (70%), Gaps = 2/233 (0%)

Query: 11  LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70
           +L+V  ++ +YG+ +AL GV + V +GE+V++IGANGAGK++L+  I G  +   GS+ F
Sbjct: 1   MLEVRDLDLHYGDAQALDGVSLDVAEGEVVAIIGANGAGKTSLIRAIAGMKKPSRGSIRF 60

Query: 71  EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLK-HFAEDVEKIFTL 129
           EG DI    +  I  L +AQ  EGR+IFP M+V ENL+MGA L   +    E +E+ + +
Sbjct: 61  EGHDIAGRASSRICDLGVAQVAEGRQIFPSMSVRENLEMGAVLPRARSKRKETLERCYEM 120

Query: 130 FPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKL 189
           FP+LK R  Q  GTLSGGEQQML+IGR LM +P+L++ DEPSLGLAP +V  +F+ I+ L
Sbjct: 121 FPKLKVRSDQAAGTLSGGEQQMLAIGRCLMGQPRLMMFDEPSLGLAPAVVSEMFKIIKTL 180

Query: 190 NEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242
           + AEG+TV LVEQN  A+L+L+ R YV+ NG+V +SG+G  LL +  VR AYL
Sbjct: 181 H-AEGMTVILVEQNVSASLKLADRGYVLENGRVVLSGTGSGLLNDDGVRQAYL 232


Lambda     K      H
   0.320    0.137    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: 195
Number of extensions: 8
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: 247
Length of database: 234
Length adjustment: 23
Effective length of query: 224
Effective length of database: 211
Effective search space:    47264
Effective search space used:    47264
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: 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