GapMind for catabolism of small carbon sources

 

Aligments for a candidate for araV in Magnetospirillum magneticum AMB-1

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_011383734.1 AMB_RS06730 nitrate ABC transporter ATP-binding protein

Query= TCDB::Q97UF2
         (371 letters)



>lcl|NCBI__GCF_000009985.1:WP_011383734.1 AMB_RS06730 nitrate ABC
           transporter ATP-binding protein
          Length = 452

 Score =  130 bits (328), Expect = 5e-35
 Identities = 76/199 (38%), Positives = 116/199 (58%), Gaps = 11/199 (5%)

Query: 17  KTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDNEAVSSPRR 76
           + E   ++ V   ++ G    +LG SG GK+T LR++AGL +   G + +    ++ P +
Sbjct: 25  RRERTVLEGVDFKLEEGEIVALLGKSGSGKSTLLRIMAGLIKANGGEVKYRGHLMTGPAK 84

Query: 77  VMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKVKEVSEELGLSGVL 136
                   GI+MVFQ++AL+P +TV +N+   L+ A V K + E +  E  + +GL G  
Sbjct: 85  --------GISMVFQSFALFPWLTVEENVELGLEAAGVAKAEREERANEAIDLIGLGGYE 136

Query: 137 NRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKIQRERKLTT 196
           + YPKELSGG  QR   ARALV  P VLLLDEPFS LD    E+ R  + ++  ERK+ T
Sbjct: 137 SAYPKELSGGMRQRVGFARALVMRPDVLLLDEPFSALDVLTSETLREDLLELWDERKIPT 196

Query: 197 ---LIVSHDPADIFAIANK 212
              L+VSH+  +  ++A++
Sbjct: 197 KGILLVSHNIEEAVSMADR 215


Lambda     K      H
   0.317    0.136    0.374 

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: 360
Number of extensions: 18
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: 371
Length of database: 452
Length adjustment: 31
Effective length of query: 340
Effective length of database: 421
Effective search space:   143140
Effective search space used:   143140
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: 50 (23.9 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