GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aglK in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate AO356_05180 AO356_05180 sugar ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc03065
         (362 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05180 AO356_05180 sugar
           ABC transporter ATP-binding protein
          Length = 386

 Score =  278 bits (710), Expect = 2e-79
 Identities = 159/363 (43%), Positives = 226/363 (62%), Gaps = 14/363 (3%)

Query: 1   MTGLLLKDIRKSYGA--VDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGG 58
           M  L L+++ K+YGA   D +  I+L IK+GEF++ VGPSGCGKSTL+  IAGLE ITGG
Sbjct: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKDGEFLILVGPSGCGKSTLMNCIAGLETITGG 60

Query: 59  DMFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAA 118
            + I  + V+ + P  R IAMVFQSYALYP M+V +N+ FG++I + ++  ID  V   A
Sbjct: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMNQSAIDEEVNRVA 120

Query: 119 DMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAK 178
            +LQ+   L+R P  LSGGQ+QRVA+GRA+ R PK++LFDEPLSNLDA LRV  R E+  
Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 179 LSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSP 238
           + +R+  TT +YVTHDQ+EAMTL D++ V+  G I+Q G P ++Y  PANLFVA FIGSP
Sbjct: 181 MHQRLK-TTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYTNPANLFVASFIGSP 239

Query: 239 AMNVIPATITATGQQTAVSLAGGKSVTLDVPTNASENG---KTASFGVRPEDLRVTEADD 295
            MN IP  +     +    L  G++   ++P    + G   +    G+RPE + +  ++ 
Sbjct: 240 PMNFIPLRLQRKDGRLLALLDSGQA-RCELPMGMQDAGLEDREVILGMRPEQIMLAGSEP 298

Query: 296 F---LFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIA-RVGRGDKVRFTADKAKLH 351
                    V + E  G  TL+++  L + +      P +A +VG    ++F  D +K+ 
Sbjct: 299 NGLPTIRAEVQVTEPTGPDTLVFV-SLNDTKVCCRLAPDVAPQVGETLTLQF--DPSKVL 355

Query: 352 LFD 354
           LFD
Sbjct: 356 LFD 358


Lambda     K      H
   0.320    0.137    0.387 

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: 14
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: 362
Length of database: 386
Length adjustment: 30
Effective length of query: 332
Effective length of database: 356
Effective search space:   118192
Effective search space used:   118192
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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 (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 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