GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Methanoculleus horonobensis T10

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_067078017.1 MCUHO_RS10540 ATP-binding cassette domain-containing protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_001602375.1:WP_067078017.1
          Length = 316

 Score = 89.7 bits (221), Expect = 7e-23
 Identities = 67/229 (29%), Positives = 110/229 (48%), Gaps = 18/229 (7%)

Query: 20  SFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGEPIQQLQ 79
           +FG   AV+     V +G I   +GPNGAGK+T  N+L+  +   KG V   G  + + +
Sbjct: 15  AFGDFTAVRGISFTVKKGEIFSFLGPNGAGKSTTINILTTLLPVQKGAVRVAGYDVAR-E 73

Query: 80  PHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVKEEKQLQEQ 139
           P ++ ++ +   FQ       L+V E M               +   ++     ++ + +
Sbjct: 74  PRKV-RKAIGIVFQDDVLDRDLTVRETM---------------EFHGRLYGIPREERRRR 117

Query: 140 AMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVNPRLIDDIC 199
              LL  V L  K  E    LSGG ++ L++ R LMT P ++ LDEP  G++P+    I 
Sbjct: 118 IDDLLRIVELEFKRDERTKNLSGGMKRRLQIARGLMTQPGVLFLDEPTQGLDPQTRMRIW 177

Query: 200 DRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQ 248
           D I   N + G T  +  H M+    L DR+ ++  G+ +  GTPAE++
Sbjct: 178 DYIRQVN-EAGTTIFLTTHYMEEADMLSDRISIIDHGRIVVSGTPAELK 225


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: 161
Number of extensions: 7
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 260
Length of database: 316
Length adjustment: 26
Effective length of query: 234
Effective length of database: 290
Effective search space:    67860
Effective search space used:    67860
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.

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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