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_03228 H281DRAFT_03228 carbohydrate ABC transporter ATP-binding protein, CUT1 family

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__Burk376:H281DRAFT_03228
          Length = 383

 Score =  335 bits (859), Expect = 1e-96
 Identities = 194/369 (52%), Positives = 244/369 (66%), Gaps = 14/369 (3%)

Query: 1   MADLKLTGVEKAYGD-VKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 59
           MA + L GV+KAYGD   V+ +++L+I + E  VF+GPSGCGKSTLLRMIAGLE +T G 
Sbjct: 1   MASISLRGVQKAYGDGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60

Query: 60  LEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAE 119
           L I G V+NDVP AQRG+AMVFQSYAL+PHMTV ENM+F LK+AK  + EID  V  AA 
Sbjct: 61  LFIGGKVMNDVPAAQRGVAMVFQSYALFPHMTVFENMAFGLKLAKTPKDEIDRKVREAAR 120

Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179
            LQL   L+R PKALSGGQRQRVAIGR+IVR P V+LFDEPLSNLDA LR  TR+EIA+L
Sbjct: 121 ILQLEALLERRPKALSGGQRQRVAIGRAIVRQPGVFLFDEPLSNLDATLRGQTRIEIARL 180

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

Query: 233 QFIGSPKMNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLM--GAAVNVGVRPEDMVE 290
            FIGSP+MN LPG+I    AQ  V   D        P+D + +    AV +GVRPE +  
Sbjct: 241 GFIGSPRMNFLPGRIASVDAQGVVVTLDHTHENVRVPADGAALQVSQAVTLGVRPEHLEF 300

Query: 291 A---APGGDYVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAE 347
           A   +   D V    V++ E LGE + ++ + P G    I K  G  +   G    L   
Sbjct: 301 ADLSSSHDDAVLSRTVSLVEQLGEHSYVHLDQPGGV-ALIAKAPGDTRLAPGDRANLRVP 359

Query: 348 PAKVHVFKD 356
               H+F +
Sbjct: 360 RHATHLFTE 368


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: 449
Number of extensions: 25
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: 383
Length adjustment: 30
Effective length of query: 343
Effective length of database: 353
Effective search space:   121079
Effective search space used:   121079
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