GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Pseudomonas fluorescens GW456-L13

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate PfGW456L13_930 Putrescine transport ATP-binding protein PotG (TC 3.A.1.11.2)

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_930
          Length = 380

 Score =  231 bits (589), Expect = 2e-65
 Identities = 133/325 (40%), Positives = 198/325 (60%), Gaps = 8/325 (2%)

Query: 4   LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63
           +K+  V K + +   + +++L+I++GE+   +G SG GKSTLLRM+AG E+ T G + +D
Sbjct: 23  VKIDRVTKKFDETIAVDDVSLEIKKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIFLD 82

Query: 64  GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQL 123
           G  + D+PP +R I M+FQSYAL+PHMTV +N++F LK  K   AE+DA V    + +Q+
Sbjct: 83  GVDITDMPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDKIPAAEVDARVAEMLKLVQM 142

Query: 124 GQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAM 183
            QY  R P  LSGGQRQRVA+ RS+ + PK+ L DEP+  LD  LR   +LE+ ++ E +
Sbjct: 143 SQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEIIERV 202

Query: 184 PESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLL 243
              T V VTHDQ EAMT+A RI ++  G IAQ+GSP+++YE P +  V +FIG+  +N+ 
Sbjct: 203 -GVTCVMVTHDQEEAMTMAERIAIMHLGWIAQIGSPIDIYETPTSRLVCEFIGN--VNIF 259

Query: 244 PGKIIGTG-AQTTVEMTDGGRAV-SDYPSDDSLMGAAVNVGVRPEDMVEAA--PGGDYVF 299
            G++I        +   D  R +   +    S+   +V   +RPE ++  A  P   Y +
Sbjct: 260 EGEVIDDAEGHAIITCKDLDRQIYVGHGISTSVQDKSVTYAIRPEKLLVTADMPTCQYNW 319

Query: 300 -EGKVAITEALGEVTLLYFEAPSGE 323
             GKV     LG  ++ Y E PSG+
Sbjct: 320 SSGKVHDIAYLGGHSVFYVELPSGK 344


Lambda     K      H
   0.316    0.135    0.379 

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: 366
Number of extensions: 17
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: 373
Length of database: 380
Length adjustment: 30
Effective length of query: 343
Effective length of database: 350
Effective search space:   120050
Effective search space used:   120050
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