GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Phaeacidiphilus oryzae TH49

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_000744815.1:WP_037572389.1
          Length = 386

 Score =  210 bits (535), Expect = 5e-59
 Identities = 125/327 (38%), Positives = 183/327 (55%), Gaps = 11/327 (3%)

Query: 3   DLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEI 62
           DL+LTG+ K +G    +  ++L I QG     +G SGCGK+T LRMI+GLE  T G + +
Sbjct: 18  DLRLTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHL 77

Query: 63  DGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQ 122
               V D  P +R +  VFQ+YAL+PH+ + EN++F L+  ++    +   VE   + ++
Sbjct: 78  GDQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLR--RRGIRSVKKPVEDMLDLVE 135

Query: 123 LGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEA 182
           LG    R P  LSGGQ+QR+A+ R+++  P+V L DEPL  LD  LR   ++E+ +++  
Sbjct: 136 LGHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLE 195

Query: 183 MPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNL 242
           +   T V+VTHDQ EAMT+A  I V+  G I Q+GSP ELYE P   FVA F+G  + NL
Sbjct: 196 V-GLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLG--QSNL 252

Query: 243 LPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEA-----APGGDY 297
           + G +        V++   GR+++   +        V +GVRPE +  A      P G  
Sbjct: 253 IAGTVESVSGD-VVQVAAHGRSLALPAARCRTTSGPVILGVRPEKVRIAKTEAEVPSGAN 311

Query: 298 VFEGKVAITEALGEVTLLYFEAPSGED 324
              GKV     +G  T    E PSGE+
Sbjct: 312 HLTGKVTDASFIGVSTQYLVELPSGEE 338


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: 353
Number of extensions: 19
Number of successful extensions: 4
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 Apr 09 2024. 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