GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Paraburkholderia bryophila 376MFSha3.1

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate H281DRAFT_02629 H281DRAFT_02629 carbohydrate ABC transporter ATP-binding protein, CUT1 family (TC 3.A.1.1.-)

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__Burk376:H281DRAFT_02629
          Length = 381

 Score =  313 bits (801), Expect = 6e-90
 Identities = 184/371 (49%), Positives = 244/371 (65%), Gaps = 15/371 (4%)

Query: 1   MADLKLTGVEKAY-GDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 59
           MA + L G++K + G+  VL ++NL+I + E  VF+GPSGCGKSTLLR++AGLE  T G 
Sbjct: 1   MAAISLRGIQKTFDGNAPVLRDLNLEIGEHEFCVFLGPSGCGKSTLLRIVAGLEDQTDGD 60

Query: 60  LEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAE 119
           + I G  +N VP A+RG+AMVFQSYAL+PHMTV ENM+F LK+A+  +AEID  V  AA 
Sbjct: 61  VSIGGRTMNSVPAAERGVAMVFQSYALFPHMTVYENMAFGLKLARTPKAEIDRKVREAAH 120

Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179
            LQL   L R P+ LSGGQRQRVAIGR+IVR+P V+LFDEPLSNLDAALR  TR+EIA+L
Sbjct: 121 VLQLDALLARKPRELSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDAALRGQTRIEIARL 180

Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVL-AG------GGIAQVGSPLELYEKPENEFVA 232
            +   ++++VYVTHDQ+EAMTLA +IV+L AG      G IAQ+G+PLELY +P ++FVA
Sbjct: 181 HQRYAQASVVYVTHDQIEAMTLADKIVLLHAGAETQRLGSIAQIGAPLELYHRPRSKFVA 240

Query: 233 QFIGSPKMNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLM-GAAVNVGVRPEDMVEA 291
            FIGSP+MN + G ++   A  +VE++  G A+        L  G  V +G+RPE +   
Sbjct: 241 GFIGSPRMNFIDG-VVERIADDSVEVSMPGTALRVLVDGRRLKPGQRVTLGIRPEHV--R 297

Query: 292 APGGDYVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKV 351
             GG         +TE LGE + L+ +   G    I K  G      G+   L       
Sbjct: 298 FDGGTQTLAVNALLTEQLGEHSYLHADHAGG--TLIAKAPGDLHVRNGERLALHLPADAC 355

Query: 352 HVF-KDGVSLH 361
           H+F +DG++LH
Sbjct: 356 HLFDEDGIALH 366


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: 437
Number of extensions: 19
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