GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Magnetospirillum magneticum AMB-1

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_043744331.1 AMB_RS11770 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC86
         (260 letters)



>NCBI__GCF_000009985.1:WP_043744331.1
          Length = 256

 Score =  183 bits (465), Expect = 3e-51
 Identities = 101/253 (39%), Positives = 151/253 (59%), Gaps = 6/253 (2%)

Query: 6   NEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGT 65
           ++++++   ++K F G  A+SDV + ++R  ++ LIGPNGAGKTT FN++T   TP  G 
Sbjct: 3   DDLIVETRSLTKEFKGFVAVSDVNLKVRRHTIHALIGPNGAGKTTCFNLVTKFLTPTRGQ 62

Query: 66  FELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTK 125
               G     T    +A+ G+ R+FQ   +F  +T LENV V    + G       F   
Sbjct: 63  ILFNGNDITHTQPAAIARQGMVRSFQISAVFGHLTVLENVRVALQRKQGKSF---QFWRS 119

Query: 126 GFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPA 185
           G    E  +  RA+EL++ VG+ ++ D  A  LSYG +R LEIA  LA DP+++ LDEP 
Sbjct: 120 GECLNE--LNARAEELIEAVGVAEYRDTPAGELSYGRKRALEIATTLALDPEMLLLDEPM 177

Query: 186 AGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQ 245
           AGM   +  +  ELI R+   NRTIL++EH++ +V  L D +TVL  G+ +AEG+ AE+ 
Sbjct: 178 AGMGTEDVRRTAELIRRVA-ANRTILMVEHNLSVVADLSDTITVLKLGRVLAEGSYAEIT 236

Query: 246 KNEKVIEAYLGTG 258
            N +V+EAY+G G
Sbjct: 237 DNPEVVEAYMGAG 249


Lambda     K      H
   0.319    0.137    0.384 

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: 193
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: 260
Length of database: 256
Length adjustment: 24
Effective length of query: 236
Effective length of database: 232
Effective search space:    54752
Effective search space used:    54752
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 (21.7 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 (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