GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Acidovorax sp. GW101-3H11

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4785
          Length = 334

 Score =  282 bits (722), Expect = 8e-81
 Identities = 168/358 (46%), Positives = 215/358 (60%), Gaps = 36/358 (10%)

Query: 1   MADLKLTGVEKAYGDV----KVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKIT 56
           MA L L  + K YG      +V+  +N +++ GE +V VGPSGCGKSTLLRM+AGLE+I+
Sbjct: 1   MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60

Query: 57  GGTLEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEA 116
           GG L I   VVND+ PAQR IAMVFQ+YALYPHMT  ENM++ LKIAK  + EI A V+ 
Sbjct: 61  GGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIKARVDK 120

Query: 117 AAEKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEI 176
           AA+ L+LG  L+R P+ LSGGQRQRVA+GR+IVR P+V+LFDEPLSNLDA LR  TRLEI
Sbjct: 121 AAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRLEI 180

Query: 177 AQLKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIG 236
            +L   +   T ++VTHDQVEAMTLA R++V+  G + Q G+P E+Y  P   FVA FIG
Sbjct: 181 QKLHREL-GITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVASFIG 239

Query: 237 SPKMNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGD 296
           SP MNLL       GAQ                           +G+RPE +   + G  
Sbjct: 240 SPPMNLLKN---APGAQ-----------------------PGTILGIRPEHLDVRSEG-- 271

Query: 297 YVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354
             +   V   E LG   L+Y    +GE   +   +G H      V  +     ++H F
Sbjct: 272 --WAVTVETVELLGAERLIYGRI-NGEQVIVRVEEGTHSPEPDSVIHVQPRADRLHAF 326


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: 364
Number of extensions: 12
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: 334
Length adjustment: 29
Effective length of query: 344
Effective length of database: 305
Effective search space:   104920
Effective search space used:   104920
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: 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