GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natE in Burkholderia phytofirmans PsJN

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 BPHYT_RS04430 BPHYT_RS04430 amino acid ABC transporter ATPase

Query= TCDB::Q8YT15
         (247 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS04430 BPHYT_RS04430 amino acid
           ABC transporter ATPase
          Length = 244

 Score =  209 bits (532), Expect = 4e-59
 Identities = 115/243 (47%), Positives = 155/243 (63%), Gaps = 11/243 (4%)

Query: 11  LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70
           +L + N+HAGY K V +L G++  V    +VT+IG NGAGK+T  + I G++ P  G+IT
Sbjct: 1   MLSIRNLHAGYGK-VKVLHGISIDVPKASVVTLIGSNGAGKTTTMRAISGMIRPSAGEIT 59

Query: 71  F----KGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKD-- 124
                  K I  L S++I RLG+ + P+   VF ++SV +NL +GAF R  S +P  D  
Sbjct: 60  MGVGTDAKRIDALDSHRIARLGLAHSPEGRRVFATMSVTDNLILGAFPRLTSARPRGDVK 119

Query: 125 ----KIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVT 180
               +   MFPRL +RR Q AGTLSGGE+QMLAM +A+M+ P L++LDEPS  L+PILV 
Sbjct: 120 ADLERAIEMFPRLKERRHQLAGTLSGGEQQMLAMARAIMMNPDLVLLDEPSMGLAPILVE 179

Query: 181 QVFEQVKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELY 240
           +VF  +  +  +G  ++LVEQ A  AL +AD GYVLE+GR A  GP  EL  DP V   Y
Sbjct: 180 EVFRIIGNLKSQGVTMLLVEQFAAAALNVADYGYVLENGRIAAHGPATELRNDPSVKAAY 239

Query: 241 LGA 243
           LGA
Sbjct: 240 LGA 242


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: 8
Number of successful extensions: 4
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: 244
Length adjustment: 24
Effective length of query: 223
Effective length of database: 220
Effective search space:    49060
Effective search space used:    49060
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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