GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA3 in Escherichia coli BW25113

Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate 17201 b3128 (D)-galactarate dehydrogenase (NCBI)

Query= reanno::BFirm:BPHYT_RS34230
         (431 letters)



>FitnessBrowser__Keio:17201
          Length = 523

 Score =  144 bits (364), Expect = 5e-39
 Identities = 122/413 (29%), Positives = 184/413 (44%), Gaps = 47/413 (11%)

Query: 9   TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPPVH-LI 67
           T EGY   DG  G +N++ +   V C   V   +V      L         + P V  ++
Sbjct: 119 TFEGYRNADGSVGTKNLLGITTSVHCVAGVVDYVVKIIERDL-------LPKYPNVDGVV 171

Query: 68  GFPGCYPNGYAE---------KMLERLTTHPNVGA-VLFVSLGCESMNKHYLV----DVV 113
           G    Y  G A          + +  ++ +PN G  V+ + LGCE +    L+    DV 
Sbjct: 172 GLNHLYGCGVAINAPAAVVPIRTIHNISLNPNFGGEVMVIGLGCEKLQPERLLTGTDDVQ 231

Query: 114 RASGRPVEVLTIQEKG--GTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGS 171
                   ++++Q++   G +S ++  +       ++L  +Q+     SELV+G  CGGS
Sbjct: 232 AIPVESASIVSLQDEKHVGFQSMVEDILQIAERHLQKLNQRQRETCPASELVVGMQCGGS 291

Query: 172 DGTSGITANPAVGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAK 231
           D  SG+TANPAVG A D L+  GAT +F E  E+      +  RA    +G  +   + +
Sbjct: 292 DAFSGVTANPAVGYASDLLVRCGATVMFSEVTEVRDAIHLLTPRAVNEEVGKRL---LEE 348

Query: 232 AARYYSILGHGSF------AVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTG 285
              Y + L  G        + GN  GGL    EK+LG+ AKSG S IV ++ PG  P   
Sbjct: 349 MEWYDNYLNMGKTDRSANPSPGNKKGGLANVVEKALGSIAKSGKSAIVEVLSPGQRPTKR 408

Query: 286 GLYLLDVVPDGEPRFGFPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCAN 345
           GL            +     SD     + +A G  V +FTTGRG+  G    PVIK+   
Sbjct: 409 GLI-----------YAATPASDFVCGTQQVASGITVQVFTTGRGTPYGLMAVPVIKMATR 457

Query: 346 PATYRNLSGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGHQ 398
                     MD++AG I  G  T++EVG ++F   + V+ G   K +T   Q
Sbjct: 458 TELANRWFDLMDINAGTIATGEETIEEVGWKLFHFILDVASG---KKKTFSDQ 507


Lambda     K      H
   0.318    0.137    0.408 

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: 613
Number of extensions: 33
Number of successful extensions: 4
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: 431
Length of database: 523
Length adjustment: 33
Effective length of query: 398
Effective length of database: 490
Effective search space:   195020
Effective search space used:   195020
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 (21.7 bits)
S2: 51 (24.3 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