GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Lysobacter daejeonensis GH1-9

Align NatE, 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_036134248.1 N800_RS01150 ATP-binding cassette domain-containing protein

Query= TCDB::Q8YT15
         (247 letters)



>NCBI__GCF_000768355.1:WP_036134248.1
          Length = 309

 Score =  105 bits (261), Expect = 1e-27
 Identities = 66/206 (32%), Positives = 112/206 (54%), Gaps = 9/206 (4%)

Query: 24  DVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGKNIAGLKSNQ 83
           D+  +  V+  V  G +   +GPNG+GKST  + + GLLTP  G +   G +I   +  +
Sbjct: 12  DLVAVDAVDLDVPRGHVYGFLGPNGSGKSTTIRMLCGLLTPSAGNVRVLGLDIP--REAE 69

Query: 84  IVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMFPR--LSDRRRQRA 141
            +RL + Y+ Q  ++F  L+V ENLE  A ++  S    + +I  +  +    DR RQ A
Sbjct: 70  ALRLRIGYMTQRFSLFEDLTVHENLEFMATVQGLSRHDARRRIDELLQQYHFQDRSRQLA 129

Query: 142 GTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQEGTAIILVEQ 201
           GT+SGG++Q LA+  +++  P LL LDEP++A+ P      +E++ ++   GT +++   
Sbjct: 130 GTMSGGQKQRLALACSVVHRPELLFLDEPTSAVDPESRRDFWEKLFELADAGTTLLVSTH 189

Query: 202 NARKA-----LEMADRGYVLESGRDA 222
              +A     L + DRG ++  G  A
Sbjct: 190 YMDEAERCHRLAILDRGVLVADGTPA 215


Lambda     K      H
   0.317    0.136    0.377 

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: 182
Number of extensions: 11
Number of successful extensions: 2
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: 247
Length of database: 309
Length adjustment: 25
Effective length of query: 222
Effective length of database: 284
Effective search space:    63048
Effective search space used:    63048
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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