GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS26365
          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:

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