GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Pseudomonas fluorescens FW300-N1B4

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)

Query= BRENDA::Q8NMV1
         (376 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115
          Length = 381

 Score =  276 bits (705), Expect = 9e-79
 Identities = 146/304 (48%), Positives = 204/304 (67%), Gaps = 16/304 (5%)

Query: 21  VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIA 80
           ++  +LEIA GEF+V VGPSGCGKST LR++AGL+++  G + I  + V  + PR+R + 
Sbjct: 19  LRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGRRVNDLEPRERGVG 78

Query: 81  MVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQ 140
           MVFQ+YALYPHM+V +N+ F LK+A   +  + +RV + A  L L + L+RKPK LSGGQ
Sbjct: 79  MVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDKLLQRKPKELSGGQ 138

Query: 141 RQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEAL 200
           RQRVAMGRA+ R P + L DEPLSNLDA LRVQ R +IA L  +LG T +YVTHDQ EA+
Sbjct: 139 RQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGSTMIYVTHDQVEAM 198

Query: 201 TMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATS----- 255
           T+ D+I VL  G ++QVG+PRELY+RPA+ FVAGF+GSP MN  +  ++    TS     
Sbjct: 199 TLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSARLQTPGETSLVDTL 258

Query: 256 --GHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSD 313
             G   +      LAA TP     +++G RPE + +    ++ D +  + +  VE LGS+
Sbjct: 259 VWGITSLPFDSSNLAAGTP-----LSLGIRPEHVSL----KAADGTAGVVVTAVEYLGSE 309

Query: 314 SFLY 317
           ++++
Sbjct: 310 TYVH 313


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: 394
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: 381
Length adjustment: 30
Effective length of query: 346
Effective length of database: 351
Effective search space:   121446
Effective search space used:   121446
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