GapMind for catabolism of small carbon sources

 

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

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Pf1N1B4_4847 Various polyols ABC transporter, ATP-binding component

Query= BRENDA::Q8NMV1
         (376 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4847 Various polyols ABC
           transporter, ATP-binding component
          Length = 367

 Score =  298 bits (764), Expect = 1e-85
 Identities = 161/323 (49%), Positives = 214/323 (66%), Gaps = 14/323 (4%)

Query: 1   MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60
           MA +  K+    + G     +K  +LE+ D EF+V VGPSGCGKST LR++AGLE V+ G
Sbjct: 1   MANLKIKNLQKGFEGFS--IIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGG 58

Query: 61  AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120
            I +  +D+T V+P  RD+AMVFQ YALYPHM+V +NM FAL +AG ++ E+ K+V EAA
Sbjct: 59  TIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVGEAA 118

Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180
             L L   LERKPK LSGGQRQRVA+GRAIVRNP++FL DEPLSNLDA LRVQ R ++  
Sbjct: 119 RILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLR 178

Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240
           L ++L  T +YVTHDQ EA+TM D++ VL  G ++QVG+P +LY +PAN+FVAGF+G+P 
Sbjct: 179 LHKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPK 238

Query: 241 MNL--GTFSVKDGDA----TSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGE 294
           M    G  +  +G +         RI L    L+       G +T+G RPE LE+   G 
Sbjct: 239 MGFLKGKVTRVNGQSCEVLLDAGTRITL---PLSGANLSVGGAVTLGIRPEHLELAQPG- 294

Query: 295 STDLSIPIKLDFVEELGSDSFLY 317
             D ++ +  D  E LGSD+F +
Sbjct: 295 --DCTLQVTADVSERLGSDTFCH 315


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: 397
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: 376
Length of database: 367
Length adjustment: 30
Effective length of query: 346
Effective length of database: 337
Effective search space:   116602
Effective search space used:   116602
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: 49 (23.5 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