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_011384838.1 AMB_RS12350 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>NCBI__GCF_000009985.1:WP_011384838.1
          Length = 234

 Score =  217 bits (553), Expect = 1e-61
 Identities = 112/233 (48%), Positives = 159/233 (68%), Gaps = 2/233 (0%)

Query: 11  LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70
           +L V  ++ +YG+ +ALAGV   V  G I +++GANGAGK++L+  I G    R GS+ F
Sbjct: 1   MLDVRDLDLFYGDAQALAGVSFTVPDGSITAIVGANGAGKTSLIRAIAGMEPPRAGSIRF 60

Query: 71  EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFA-EDVEKIFTL 129
           +G DIT   + EI  L + Q  EGR++FP M+V +NL++GA +   +  A + +E+++ +
Sbjct: 61  DGHDITGKESFEICDLGLGQVAEGRQVFPTMSVQDNLELGAMVPRARKLATQSLERVWEM 120

Query: 130 FPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKL 189
           FPRL ER  Q  GTLSGGEQQML+IGR LM RPK+++ DEPSLGL+P +V  +F  IR+L
Sbjct: 121 FPRLLERRKQLAGTLSGGEQQMLAIGRCLMGRPKMIMFDEPSLGLSPAMVHEVFAIIRRL 180

Query: 190 NEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242
           +E +G+TV LVEQN   +L ++  A V+ NG V M G G +LL +  VRAAYL
Sbjct: 181 HE-DGMTVVLVEQNVAVSLHMADHACVLENGHVVMEGRGADLLGDDRVRAAYL 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: 201
Number of extensions: 9
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