GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livJ in Klebsiella michiganensis M5al

Align leucine-specific-binding protein LivK (characterized)
to candidate BWI76_RS26350 BWI76_RS26350 branched chain amino acid ABC transporter substrate-binding protein

Query= CharProtDB::CH_107418
         (369 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS26350 BWI76_RS26350 branched chain
           amino acid ABC transporter substrate-binding protein
          Length = 369

 Score =  674 bits (1740), Expect = 0.0
 Identities = 332/369 (89%), Positives = 350/369 (94%)

Query: 1   MKRNAKTIIAGMIALAISHTAMADDIKVAVVGAMSGPIAQWGDMEFNGARQAIKDINAKG 60
           MKRNAKT+IAG++ALA+S  A A DIKVAVVGAMSGP+AQWGDMEFNGARQAIKDINA+G
Sbjct: 1   MKRNAKTVIAGLVALAMSQAAFAKDIKVAVVGAMSGPVAQWGDMEFNGARQAIKDINAQG 60

Query: 61  GIKGDKLVGVEYDDACDPKQAVAVANKIVNDGIKYVIGHLCSSSTQPASDIYEDEGILMI 120
           GIKGDKLV VEYDDACDPKQAVAVANKIVNDGI+YVIGHLCSSSTQPASDIYEDEGILMI
Sbjct: 61  GIKGDKLVAVEYDDACDPKQAVAVANKIVNDGIQYVIGHLCSSSTQPASDIYEDEGILMI 120

Query: 121 SPGATNPELTQRGYQHIMRTAGLDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGLARS 180
           SPGATNPELTQRGYQ+IMRTAGLDSSQGPTAAKYI+ETVKPQRIAIIHDKQQYGEGLARS
Sbjct: 121 SPGATNPELTQRGYQYIMRTAGLDSSQGPTAAKYIMETVKPQRIAIIHDKQQYGEGLARS 180

Query: 181 VQDGLKAANANVVFFDGITAGEKDFSALIARLKKENIDFVYYGGYYPEMGQMLRQARSVG 240
           VQ+ LK   AN+VFFDGITAGEKDFSAL+ARLKKENIDFVYYGGYYPEMGQMLRQARSVG
Sbjct: 181 VQESLKKGGANIVFFDGITAGEKDFSALLARLKKENIDFVYYGGYYPEMGQMLRQARSVG 240

Query: 241 LKTQFMGPEGVGNASLSNIAGDAAEGMLVTMPKRYDQDPANQGIVDALKADKKDPSGPYV 300
           LKT FMGPEGVGNASLSNIAGDAAEGMLVTMPKRYDQDPAN  IVDALKA+KKDPSGPYV
Sbjct: 241 LKTVFMGPEGVGNASLSNIAGDAAEGMLVTMPKRYDQDPANSAIVDALKAEKKDPSGPYV 300

Query: 301 WITYAAVQSLATALERTGSDEPLALVKDLKANGANTVIGPLNWDEKGDLKGFDFGVFQWH 360
           WITYAAVQSLA A++R  S EPL L+KDLKA+GA TVIGPLNWDEKGDLKGF+FGVFQWH
Sbjct: 301 WITYAAVQSLAQAMDRAASQEPLDLIKDLKAHGAKTVIGPLNWDEKGDLKGFEFGVFQWH 360

Query: 361 ADGSSTAAK 369
           ADGSST AK
Sbjct: 361 ADGSSTLAK 369


Lambda     K      H
   0.315    0.133    0.386 

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: 629
Number of extensions: 13
Number of successful extensions: 1
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: 369
Length of database: 369
Length adjustment: 30
Effective length of query: 339
Effective length of database: 339
Effective search space:   114921
Effective search space used:   114921
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 (21.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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