GapMind for catabolism of small carbon sources

 

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

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AO356_28380 AO356_28380 ABC transporter permease

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28380
          Length = 355

 Score =  127 bits (318), Expect = 6e-34
 Identities = 100/340 (29%), Positives = 161/340 (47%), Gaps = 36/340 (10%)

Query: 11  GAVALLVLPLILQSF--GNAWVRIADLALLYVLLA-LGLNIVVGYAGLLDLGYVAFYAVG 67
           G  ALL+   ++  +   + W     +  L + LA LGLN++ GYAG L LG  AF AVG
Sbjct: 28  GLAALLLFAFVVVPWLGNDYWFSAILIPFLVLSLAGLGLNLLTGYAGQLSLGSAAFMAVG 87

Query: 68  AYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDY 127
           A+            N     A  P      L + I +  L AA    + G P+L+++G Y
Sbjct: 88  AFA---------TYNLEIRVAGLP------LLVSIALGGLTAALVAVLFGLPSLRIKGFY 132

Query: 128 LAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVT 187
           L + TL     +   L       N +               G+    RL+VFG ++++  
Sbjct: 133 LLVSTLAAQFFVTWALTRFSWFSNNSAS-------------GVISAPRLDVFGVNLDAPA 179

Query: 188 LYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASF 247
             Y L L +VV    +   L  S +GR WMA+R+ + AA  +GI     KLLAF +   F
Sbjct: 180 GRYLLTLSVVVALFWLGKNLVRSELGRNWMAVRDMDTAAAVIGIALAKTKLLAFAISGFF 239

Query: 248 GGVSGAMFG-AFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRY 306
            GV+GA++  A+ G V P  F L  S  I+ ++++GG+G + G  LGA  +   P +L  
Sbjct: 240 LGVAGALWAFAYLGTVEPHGFDLNRSFQILFIIIIGGLGSLLGNFLGAAFIVLFPVLLSN 299

Query: 307 VAG--PLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344
           +    P   +  G++++  L++++    +I+ ++  P GL
Sbjct: 300 LVSLLPGGLVDAGQVEN--LQKMIFGALIILFLIKEPEGL 337


Lambda     K      H
   0.328    0.144    0.430 

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: 318
Number of extensions: 14
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: 358
Length of database: 355
Length adjustment: 29
Effective length of query: 329
Effective length of database: 326
Effective search space:   107254
Effective search space used:   107254
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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 (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