GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braC in Klebsiella michiganensis M5al

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate BWI76_RS26350 BWI76_RS26350 branched chain amino acid ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



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

 Score =  415 bits (1067), Expect = e-121
 Identities = 195/365 (53%), Positives = 272/365 (74%), Gaps = 4/365 (1%)

Query: 13  AAMAIAGFASYSMA----ADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNG 68
           A   IAG  + +M+    A  IK+A+ G ++GPVAQ+GDM+  GA  AI+ IN  GG+ G
Sbjct: 5   AKTVIAGLVALAMSQAAFAKDIKVAVVGAMSGPVAQWGDMEFNGARQAIKDINAQGGIKG 64

Query: 69  AQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSA 128
            +L  V YDDACDPKQAVAVANK+VNDG+++V+GH+CSSSTQPA+DIYEDEG+LMI+P A
Sbjct: 65  DKLVAVEYDDACDPKQAVAVANKIVNDGIQYVIGHLCSSSTQPASDIYEDEGILMISPGA 124

Query: 129 TAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKT 188
           T PE+T RGY+ I RT GLD+ QGP A K+I E  K + IA++HDKQQYGEG+A  V+++
Sbjct: 125 TNPELTQRGYQYIMRTAGLDSSQGPTAAKYIMETVKPQRIAIIHDKQQYGEGLARSVQES 184

Query: 189 VEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDAR 248
           ++  G  +  F+G+ AG+KDF+AL+++LKK  + FVY+GGY+PEMG +LRQA+  GL   
Sbjct: 185 LKKGGANIVFFDGITAGEKDFSALLARLKKENIDFVYYGGYYPEMGQMLRQARSVGLKTV 244

Query: 249 FMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAY 308
           FMGPEGVGN+ ++ IAGDA+EGML T+P+ ++QDP N A++DA KA+ +DPSG +V   Y
Sbjct: 245 FMGPEGVGNASLSNIAGDAAEGMLVTMPKRYDQDPANSAIVDALKAEKKDPSGPYVWITY 304

Query: 309 SAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWHKDAT 368
           +AV  +A+ +++A   +P  + + L+A+  +T  G L +DEKGDLK F+F V++WH D +
Sbjct: 305 AAVQSLAQAMDRAASQEPLDLIKDLKAHGAKTVIGPLNWDEKGDLKGFEFGVFQWHADGS 364

Query: 369 RTEVK 373
            T  K
Sbjct: 365 STLAK 369


Lambda     K      H
   0.316    0.133    0.377 

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: 464
Number of extensions: 25
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: 373
Length of database: 369
Length adjustment: 30
Effective length of query: 343
Effective length of database: 339
Effective search space:   116277
Effective search space used:   116277
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: 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