GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Collimonas arenae Ter10

Align NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_061535047.1 CAter10_RS21450 ABC transporter ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_001584165.1:WP_061535047.1
          Length = 256

 Score =  170 bits (431), Expect = 2e-47
 Identities = 97/251 (38%), Positives = 142/251 (56%), Gaps = 11/251 (4%)

Query: 11  LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70
           +L    L K F G  AV    ++V +G I  LIGPNGAGKTT FNLL+ F+ P  G+++F
Sbjct: 5   ILETKNLTKEFRGFTAVNGVNLQVQRGHIHALIGPNGAGKTTCFNLLTKFLVPTSGQILF 64

Query: 71  DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGE--NFWQVQLQPQV 128
           +G  I    P QIA+QG++R+FQ++     L+V+EN+ +  Q+  G   +FW+       
Sbjct: 65  NGRDITTDAPAQIARQGIIRSFQISAVFPHLTVMENVRIGLQRTLGTSFHFWKSG----- 119

Query: 129 VVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAA 188
             K   QL E+AM LL  V L + A      L  G+++ LE+   L   P+L+LLDEP  
Sbjct: 120 --KSLAQLNERAMALLAEVDLTEFADTLTVDLPYGRKRALEIATTLAMEPELMLLDEPTQ 177

Query: 189 GVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQ 248
           G+    +D +    L      G T L++EHNM+V+  +CD++ VL  G  LA+G   E+ 
Sbjct: 178 GMGHEDVDRV--TALIKKVSAGRTILMVEHNMNVVSGICDKISVLQRGAMLAEGRYEEVS 235

Query: 249 TNSQVLEAYLG 259
            N  V+EAY+G
Sbjct: 236 KNPLVMEAYMG 246


Lambda     K      H
   0.319    0.136    0.391 

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: 136
Number of extensions: 6
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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