GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livJ in Klebsiella michiganensis M5al

Align Leu/Ile/Val-binding protein LivJ aka B3460 aka LIV-BP, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate BWI76_RS26365 BWI76_RS26365 branched chain amino acid ABC transporter substrate-binding protein

Query= TCDB::P0AD96
         (367 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS26365 BWI76_RS26365 branched chain
           amino acid ABC transporter substrate-binding protein
          Length = 372

 Score =  693 bits (1789), Expect = 0.0
 Identities = 345/367 (94%), Positives = 356/367 (97%)

Query: 1   MNIKGKALLAGCIALAFSNMALAEDIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKG 60
           MN+KGKALLAGCIAL  S  A+AEDIKVAVVGAMSGPVAQYGDQEFTGAEQA+ADINAKG
Sbjct: 6   MNMKGKALLAGCIALIMSGTAMAEDIKVAVVGAMSGPVAQYGDQEFTGAEQAIADINAKG 65

Query: 61  GIKGNKLQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMI 120
           GIKGNKLQ+VKYDDACDPKQAVAVANKV+NDGIKYVIGHLCSSSTQPASDIYEDEG+LMI
Sbjct: 66  GIKGNKLQMVKYDDACDPKQAVAVANKVINDGIKYVIGHLCSSSTQPASDIYEDEGVLMI 125

Query: 121 TPAATAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARA 180
           TPAATAPELTARGY LILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARA
Sbjct: 126 TPAATAPELTARGYHLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARA 185

Query: 181 VQDGLKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAG 240
           VQD LKKG ANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQ+RAAG
Sbjct: 186 VQDNLKKGGANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQSRAAG 245

Query: 241 LKTQFMGPEGVANVSLSNIAGESAEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFV 300
           LKTQFMGPEGVANVSLSNIAG SAEG+LVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFV
Sbjct: 246 LKTQFMGPEGVANVSLSNIAGASAEGMLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFV 305

Query: 301 WTTYAALQSLQAGLNQSDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWHAN 360
           WTTYAALQSLQAGLNQS+DPAEIAKYLK  +VDTVMGPLTW+EKGDLKGFEFGVF WHAN
Sbjct: 306 WTTYAALQSLQAGLNQSEDPAEIAKYLKGATVDTVMGPLTWNEKGDLKGFEFGVFTWHAN 365

Query: 361 GTATDAK 367
           GTATDAK
Sbjct: 366 GTATDAK 372


Lambda     K      H
   0.314    0.133    0.380 

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: 631
Number of extensions: 8
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: 367
Length of database: 372
Length adjustment: 30
Effective length of query: 337
Effective length of database: 342
Effective search space:   115254
Effective search space used:   115254
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: 42 (22.0 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 paper from 2022 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