GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Echinicola vietnamensis KMM 6221, DSM 17526

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate Echvi_1497 Echvi_1497 NAD-dependent aldehyde dehydrogenases

Query= metacyc::MONOMER-15108
         (486 letters)



>FitnessBrowser__Cola:Echvi_1497
          Length = 469

 Score =  155 bits (391), Expect = 4e-42
 Identities = 102/340 (30%), Positives = 171/340 (50%), Gaps = 11/340 (3%)

Query: 142 YAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVLAEICRDAG 201
           Y    P G + +I+PWN P  L    L  A+AAG +  +KP+E +P T+ +L  +  +  
Sbjct: 97  YLQAEPKGAVLIISPWNYPFNLSVAPLVSAIAAGCSACLKPSEHSPHTSALLRRMVTELF 156

Query: 202 VPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKRLSYELGGK 261
             + V     G    S    L E P  + I FTG T  GKI+M +AAK L  ++ ELGGK
Sbjct: 157 AVEDVTIFEGGVPVTSE---LLEQP-FDHIFFTGSTEVGKIVMKAAAKNLTSVTLELGGK 212

Query: 262 NPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVAKTKEL--V 319
           +P +I    +L++  +      FIN G+ C+    ++V     + F+E   A+   +   
Sbjct: 213 SPAIIDQGFDLEDAAKKIAIGKFINSGQTCIAPDYLFVHESQKQDFIETLKAQVNRMYNA 272

Query: 320 VGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFLEPTIITG 379
            G  FD     G +I   H  R+   +K A  +G  +  GGK    L++  F+EPT+++ 
Sbjct: 273 NGKGFDRNPDYGRIIHAPHIVRLQNMLKDAQTKGAHVEFGGK--NSLDQ-QFMEPTVVSN 329

Query: 380 LTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHRVAGQIEA 439
           ++    ++KEEIFGP++ +I +   ++V++ I      L+   +T D R   +++    +
Sbjct: 330 VSEAMDLMKEEIFGPILPIITYHQLDDVIQLIQLKPKPLAVYAFTTDDRIIEQLSKNTSS 389

Query: 440 GIVWVNTWFLRDLRT--PFGGMKQSGIGREGGLHSFEFYS 477
           G + +N   ++ L +  PFGG+  SG+GR  G   F  +S
Sbjct: 390 GALVINDCAIQFLHSELPFGGIGASGMGRSHGHAGFLAFS 429


Lambda     K      H
   0.318    0.136    0.404 

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: 521
Number of extensions: 28
Number of successful extensions: 6
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: 486
Length of database: 469
Length adjustment: 34
Effective length of query: 452
Effective length of database: 435
Effective search space:   196620
Effective search space used:   196620
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