GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Thiothrix lacustris DSM 21227

Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= TCDB::Q88NY5
         (256 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  142 bits (357), Expect = 1e-38
 Identities = 82/227 (36%), Positives = 128/227 (56%), Gaps = 6/227 (2%)

Query: 11  LRMISIKNVNKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGDI 70
           +  + +KNV+K+YG    +   S E++ GE +V  GPSG GKSTL++ +  LE    G +
Sbjct: 1   MAFLELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQL 60

Query: 71  VVDGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQRKVLGRSEAEATKKGL 130
           ++DG  I    T +P  +  + MVFQ + L+PH+T+ EN++ A R +     A   +K  
Sbjct: 61  ILDGRDI----TEVPPSQRDLAMVFQSYALYPHMTVEENMSFALR-LAKVDPAIIQEKVK 115

Query: 131 ALLDRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVSEVLDV 190
              D++ L+A+ ++ P  LSGGQ+QRVAI R++   P V LFDEP S LD  +       
Sbjct: 116 MAADKLNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVE 175

Query: 191 MVQLAQE-GMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFF 236
           +  L +E G T + VTH+   A  +A+RV+ +  G I +  T  E +
Sbjct: 176 IASLHRELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELY 222


Lambda     K      H
   0.319    0.134    0.383 

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: 187
Number of extensions: 9
Number of successful extensions: 4
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: 256
Length of database: 348
Length adjustment: 27
Effective length of query: 229
Effective length of database: 321
Effective search space:    73509
Effective search space used:    73509
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: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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