GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_06394 H281DRAFT_06394 amino acid/amide ABC transporter ATP-binding protein 2, HAAT family

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__Burk376:H281DRAFT_06394
          Length = 233

 Score =  204 bits (519), Expect = 1e-57
 Identities = 108/234 (46%), Positives = 150/234 (64%), Gaps = 4/234 (1%)

Query: 11  LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70
           +L+V+ +H  Y K   ILQGV+ ++  GE VT++G NGAGKST  K I G++ P  G +T
Sbjct: 2   ILDVQQIHGFYGKS-HILQGVSLQIAEGETVTLLGRNGAGKSTTLKAIAGVVAPKNGSVT 60

Query: 71  FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMF 130
           F G  I+GL+ ++I   G+C+VP+   +F  L+VEENL +GA  R DS   L D I+ +F
Sbjct: 61  FNGATISGLQPHKIASRGVCFVPEHRGIFRLLTVEENLRLGA--RKDSPWQLDD-IYRIF 117

Query: 131 PRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQIN 190
           PRL +RR    G LSGGE+QMLA+G+ALM  P LL+LDEP   L+P++V ++  Q+K I 
Sbjct: 118 PRLKERRTNGGGQLSGGEQQMLAVGRALMNHPRLLMLDEPVEGLAPVIVEEIVAQLKLIR 177

Query: 191 QEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLGAG 244
           + G AI+LVEQN     ++ADR Y++E G    SG       D  V + YLG G
Sbjct: 178 EAGVAILLVEQNLEVCTQLADRHYIIEQGVIVYSGDNASFAADDSVKDRYLGVG 231


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: 176
Number of extensions: 9
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: 233
Length adjustment: 23
Effective length of query: 224
Effective length of database: 210
Effective search space:    47040
Effective search space used:    47040
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 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