GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Pseudomonas fluorescens FW300-N1B4

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115
          Length = 381

 Score =  311 bits (797), Expect = 2e-89
 Identities = 178/364 (48%), Positives = 239/364 (65%), Gaps = 8/364 (2%)

Query: 4   LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63
           LKL  V K  G +++L +++L+I  GE +VFVGPSGCGKSTLLR+IAGL+ I GG L ID
Sbjct: 4   LKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLID 63

Query: 64  GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQL 123
           G  VND+ P +RG+ MVFQSYALYPHM+V +N+SF LK+AK  +  +   V   A+ LQL
Sbjct: 64  GRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQL 123

Query: 124 GQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAM 183
            + L R PK LSGGQRQRVA+GR++ R+P + LFDEPLSNLDA+LRV  R EIA+L + +
Sbjct: 124 DKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRL 183

Query: 184 PESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLL 243
             STM+YVTHDQVEAMTLA +IVVL GG + QVGSP ELYE+P + FVA F+GSP+MN L
Sbjct: 184 -GSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFL 242

Query: 244 PGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDM-VEAAPGGDYVFEGK 302
             ++   G  + V+    G     + S +   G  +++G+RPE + ++AA G   V    
Sbjct: 243 SARLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADGTAGVV--- 299

Query: 303 VAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF-KDGVSL- 360
           V   E LG  T ++ E    ++P I + +       G    L  +   +H+F  DGV+L 
Sbjct: 300 VTAVEYLGSETYVHLET-GQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADGVALS 358

Query: 361 HYPH 364
            +PH
Sbjct: 359 RHPH 362


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: 382
Number of extensions: 15
Number of successful extensions: 2
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: 381
Length adjustment: 30
Effective length of query: 343
Effective length of database: 351
Effective search space:   120393
Effective search space used:   120393
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