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_593 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_593
          Length = 386

 Score =  275 bits (702), Expect = 2e-78
 Identities = 162/361 (44%), Positives = 216/361 (59%), Gaps = 11/361 (3%)

Query: 1   MADLKLTGVEKAYGD--VKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGG 58
           MA L+L  V K YG      L NI L I  GE ++ VGPSGCGKSTL+  IAGLE I+GG
Sbjct: 1   MATLELRNVNKTYGAGLPDTLKNIELKINDGEFLILVGPSGCGKSTLMNCIAGLENISGG 60

Query: 59  TLEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAA 118
            + +D   ++ + P  R IAMVFQSYALYP M+VR+N++F LKI K   AEID  V   A
Sbjct: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVA 120

Query: 119 EKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQ 178
           + LQ+   L R P  LSGGQ+QRVA+GR++ R PK+YLFDEPLSNLDA LRV  R E+  
Sbjct: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 179 LKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSP 238
           + + + ++T VYVTHDQ+EAMTL  ++ V+  G I Q G+P ++Y  P N FVA FIGSP
Sbjct: 181 MHQRL-KTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSP 239

Query: 239 KMNLLPGKIIGTGAQTTVEMTDGGRAVSDYP---SDDSLMGAAVNVGVRPEDMVEAA--P 293
            MN +P ++     +  V + D G+A  + P    D  L    V +G+RPE +V A   P
Sbjct: 240 PMNFIPLRLQRKDGR-LVALLDSGQARCELPLGMQDAGLEDREVILGMRPEQIVLAGSEP 298

Query: 294 GGDYVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHV 353
            G      +V +TE  G  TL++      +     +L        G+   L  +P+KV +
Sbjct: 299 NGLPTIRAEVQVTEPTGPDTLVFVNL--NDTKVCCRLAPDVAPAVGETLTLQFDPSKVLL 356

Query: 354 F 354
           F
Sbjct: 357 F 357


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: 404
Number of extensions: 22
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: 386
Length adjustment: 30
Effective length of query: 343
Effective length of database: 356
Effective search space:   122108
Effective search space used:   122108
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