GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Pseudomonas fluorescens FW300-N2C3

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate AO356_05180 AO356_05180 sugar ABC transporter ATP-binding protein

Query= BRENDA::Q8NMV1
         (376 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05180
          Length = 386

 Score =  303 bits (775), Expect = 7e-87
 Identities = 169/381 (44%), Positives = 233/381 (61%), Gaps = 22/381 (5%)

Query: 1   MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60
           MAT+  ++ + +Y      T+K   L I DGEFL+LVGPSGCGKST +  +AGLE +T G
Sbjct: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKDGEFLILVGPSGCGKSTLMNCIAGLETITGG 60

Query: 61  AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120
           AI IGD+DV+ ++P+DRDIAMVFQ+YALYP M+V EN+ F LKI   +Q  I++ V+  A
Sbjct: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMNQSAIDEEVNRVA 120

Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180
             L +   L RKP  LSGGQ+QRVAMGRA+ R P+++L DEPLSNLDAKLRV+ RT++  
Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240
           + ++L  TTVYVTHDQ EA+T+GD++AV+KDG +QQ G P+++Y  PAN+FVA FIGSP 
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYTNPANLFVASFIGSPP 240

Query: 241 MNLGTFSV--KDGD----ATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGE 294
           MN     +  KDG       SG AR +L P  +     ED   + +G RPE + +     
Sbjct: 241 MNFIPLRLQRKDGRLLALLDSGQARCEL-PMGMQDAGLEDR-EVILGMRPEQIMLAGSEP 298

Query: 295 STDLSIPIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGSV 354
           +   +I  ++   E  G D+ ++  L                 ++  R AP+ AP  G  
Sbjct: 299 NGLPTIRAEVQVTEPTGPDTLVFVSL--------------NDTKVCCRLAPDVAPQVGET 344

Query: 355 FHARIVEGGQHNFSASTGKRL 375
              +        F A +G+RL
Sbjct: 345 LTLQFDPSKVLLFDAQSGERL 365


Lambda     K      H
   0.316    0.135    0.380 

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: 419
Number of extensions: 12
Number of successful extensions: 1
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: 376
Length of database: 386
Length adjustment: 30
Effective length of query: 346
Effective length of database: 356
Effective search space:   123176
Effective search space used:   123176
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 (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:

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