GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natD in Paraburkholderia bryophila 376MFSha3.1

Align NatD, 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_06397 H281DRAFT_06397 amino acid/amide ABC transporter membrane protein 1, HAAT family

Query= TCDB::Q8YXD0
         (288 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_06397 H281DRAFT_06397 amino
           acid/amide ABC transporter membrane protein 1, HAAT
           family
          Length = 286

 Score =  148 bits (373), Expect = 2e-40
 Identities = 94/289 (32%), Positives = 159/289 (55%), Gaps = 14/289 (4%)

Query: 1   MDIQTIQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTFGVN 60
           M++  +Q IVNGI VG +  L AVGL++ +G+LR  NFAHG F  LGAY  +    + ++
Sbjct: 1   MNVYLLQ-IVNGIGVGMLYFLLAVGLSIVFGLLRFVNFAHGAFYMLGAYFCYQAMQWSMS 59

Query: 61  IWLSMIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTL-IIISIGLALFLRNGIILIWGGR 119
            W ++IV  +    +  + EKL+   +R + A      I++++GLAL ++   IL+WG  
Sbjct: 60  FWTALIVVPIAVGALAWVVEKLI---LRHVYAQQHEFHILVTVGLALVVQECAILVWGPL 116

Query: 120 NQNYNLP-ITPALDIFGVKV-PQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLD 177
             N  +P +   + I+G  V P+ +L V+    +    L ++L+ T++G A+RA ++  +
Sbjct: 117 GDNVAVPDMLNGVVIWGSFVYPKYRLFVIGFTAVLAALLWWVLEGTRLGSAVRAGSESTE 176

Query: 178 LAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGN 237
           +  + GI+V +V    + +     +L G +   I  V P MG   +   F  V++GG+GN
Sbjct: 177 MVSLLGINVLRVFSLVFALGAATAALAGVLAAPIRGVDPFMGIEALGVAFVVVVVGGMGN 236

Query: 238 PYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLI---MILVLLIRPKGL 283
             GA+    ++GIVQ V    + + + +G  L+I   M  VLL+RP GL
Sbjct: 237 FLGALVGGLLVGIVQSV----MSTLWPEGARLMIYVAMAAVLLLRPNGL 281


Lambda     K      H
   0.328    0.144    0.426 

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: 255
Number of extensions: 16
Number of successful extensions: 3
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: 288
Length of database: 286
Length adjustment: 26
Effective length of query: 262
Effective length of database: 260
Effective search space:    68120
Effective search space used:    68120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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