GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Marinobacter adhaerens HP15

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__Marino:GFF3011
          Length = 372

 Score =  266 bits (681), Expect = 5e-76
 Identities = 146/296 (49%), Positives = 201/296 (67%), Gaps = 8/296 (2%)

Query: 1   MADLKLTGVEKAYGDV--KVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGG 58
           M+ L+L  + K Y  V  + L  I++DI  GE ++ VGPSGCGKSTL+  IAGLE IT G
Sbjct: 1   MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60

Query: 59  TLEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAA 118
           ++ +DG  ++ + P  R IAMVFQSYALYP M+VREN++F LKI    + EID  VE  A
Sbjct: 61  SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120

Query: 119 EKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQ 178
           + LQ+   +++ P  LSGGQ+QRVA+GR++ R P++YLFDEPLSNLDA LRV  R EI +
Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180

Query: 179 LKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSP 238
           L + + ++T+VYVTHDQ+EAMTLA RI VL  G + Q+G+P E+Y++PEN FVA F+GSP
Sbjct: 181 LHQRL-KTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSP 239

Query: 239 KMNLLPGKI-IGTGAQTTVEMTDGGRAVSDYPSDDSL---MGAAVNVGVRPEDMVE 290
            M+ +P  +  G G        + GR+V   P  + L   +G  V +G+RPE + +
Sbjct: 240 AMSFVPVTVEQGEGGLQAEVRGNDGRSVK-LPVPEFLADRVGKKVILGIRPEHITQ 294


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: 23
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: 372
Length adjustment: 30
Effective length of query: 343
Effective length of database: 342
Effective search space:   117306
Effective search space used:   117306
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