GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Escherichia coli BW25113

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate 1937025 b3460 leucine/isoleucine/valine transporter subunit (NCBI)

Query= SwissProt::P21175
         (373 letters)



>FitnessBrowser__Keio:1937025
          Length = 367

 Score =  418 bits (1074), Expect = e-121
 Identities = 198/363 (54%), Positives = 272/363 (74%), Gaps = 3/363 (0%)

Query: 11  LFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQ 70
           L A      F++ ++A D IK+A+ G ++GPVAQYGD +  GA  A+  IN  GG+ G +
Sbjct: 8   LLAGCIALAFSNMALAED-IKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGIKGNK 66

Query: 71  LEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATA 130
           L+ V YDDACDPKQAVAVANKVVNDG+K+V+GH+CSSSTQPA+DIYEDEG+LMITP+ATA
Sbjct: 67  LQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMITPAATA 126

Query: 131 PEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVE 190
           PE+T+RGY+LI RT GLD+ QGP A K+I E+ K + IA++HDKQQYGEG+A  V+  ++
Sbjct: 127 PELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQDGLK 186

Query: 191 DAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFM 250
                V  F+G+ AG+KDF+ L+++LKK  + FVY+GGYHPEMG +LRQA+ AGL  +FM
Sbjct: 187 KGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLKTQFM 246

Query: 251 GPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYSA 310
           GPEGV N  ++ IAG+++EG+L T P+ ++Q P NK ++DA KAK QDPSG FV   Y+A
Sbjct: 247 GPEGVANVSLSNIAGESAEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFVWTTYAA 306

Query: 311 VTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWHKDATRT 370
           +  +  G+ ++   DP ++A+ L+AN+ +T  G L +DEKGDLK F+F V++WH + T T
Sbjct: 307 LQSLQAGLNQSD--DPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWHANGTAT 364

Query: 371 EVK 373
           + K
Sbjct: 365 DAK 367


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: 466
Number of extensions: 19
Number of successful extensions: 2
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: 367
Length adjustment: 30
Effective length of query: 343
Effective length of database: 337
Effective search space:   115591
Effective search space used:   115591
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:

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