GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natE in Magnetospirillum magneticum AMB-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 WP_011384207.1 AMB_RS09120 ABC transporter ATP-binding protein

Query= TCDB::Q8YT15
         (247 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384207.1 AMB_RS09120 ABC
           transporter ATP-binding protein
          Length = 237

 Score =  203 bits (516), Expect = 3e-57
 Identities = 109/239 (45%), Positives = 158/239 (66%), Gaps = 5/239 (2%)

Query: 11  LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70
           +L +E++H+GY + +  L GV+  V  GE+V ++G NGAGK+TL  TI G      G + 
Sbjct: 1   MLRIESLHSGYGR-IQALHGVDINVAEGEIVALVGANGAGKTTLLMTICGNPRATAGTVR 59

Query: 71  FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDS--LQPLKDKIFA 128
             G++I GL ++ I+R G+ + P+   +F  +SV ENL+MGA   N +   Q L +++  
Sbjct: 60  LAGEDITGLATHHIMRRGLAHSPEGRRIFARMSVLENLQMGAARGNPAHFAQDL-ERVLG 118

Query: 129 MFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQ 188
           +FPRL +R  QR GTLSGGE+QMLA+G+ALM  P +L+LDEPS  L+P++V Q+FE V  
Sbjct: 119 LFPRLEERLAQRGGTLSGGEQQMLAIGRALMSRPKILLLDEPSLGLAPLVVRQIFEIVAT 178

Query: 189 INQE-GTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLGAGKG 246
           IN+E G  + LVEQNA  AL +A RGYV+ +G+  +SG G ELL + ++   YLG G G
Sbjct: 179 INREQGVTVFLVEQNAHHALRLAHRGYVMVNGKVTLSGTGAELLANEEIRAHYLGGGHG 237


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: 237
Length adjustment: 23
Effective length of query: 224
Effective length of database: 214
Effective search space:    47936
Effective search space used:    47936
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, 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