GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Methylocystis bryophila S285

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_085770502.1 B1812_RS04380 ABC transporter ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_002117405.1:WP_085770502.1
          Length = 293

 Score =  148 bits (374), Expect = 1e-40
 Identities = 87/249 (34%), Positives = 139/249 (55%), Gaps = 2/249 (0%)

Query: 12  LAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFD 71
           LA + +  SFGGI+A+ E    VA G I  +IGPNGAGK++L N+++   RPD GR+  D
Sbjct: 35  LALTNISLSFGGIQALSEIDFSVAAGEICSIIGPNGAGKSSLINVITGLYRPDWGRIQLD 94

Query: 72  GEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVK 131
                ++   ++A  G+ RTFQ       LSV +N+ +     T  + W  Q+      +
Sbjct: 95  KNSFSRMPTERLASLGVARTFQNLALFRGLSVFDNIAVGRVSAT-RSHWLEQVFGLPRAR 153

Query: 132 EEKQLQEQAM-FLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190
            ++   E  +  +L  +GL +     AG L  G +K +E+ RAL   P+L+LLDEP AG+
Sbjct: 154 ADRLATEIIVEEMLVFLGLGQVRNRIAGTLPYGMQKRVELARALAIRPRLLLLDEPMAGM 213

Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTN 250
                 ++ + I     + G + ++IEH++ V+M L DRV VL  G+ +ADG P+++  +
Sbjct: 214 TAGEKAEMGEFIQLTRDRFGASIVLIEHDIGVVMELSDRVAVLDYGRKIADGPPSDVMND 273

Query: 251 SQVLEAYLG 259
             V++AYLG
Sbjct: 274 EAVIDAYLG 282


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: 150
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: 293
Length adjustment: 25
Effective length of query: 235
Effective length of database: 268
Effective search space:    62980
Effective search space used:    62980
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 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