GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Cronobacter universalis NCTC 9529

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_038857023.1 AFK65_RS11195 bifunctional acetaldehyde-CoA/alcohol dehydrogenase

Query= ecocyc::EG12293-MONOMER
         (383 letters)



>NCBI__GCF_001277175.1:WP_038857023.1
          Length = 892

 Score =  199 bits (507), Expect = 2e-55
 Identities = 129/383 (33%), Positives = 205/383 (53%), Gaps = 35/383 (9%)

Query: 18  SLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENV 77
           SL  A++ +   G  R +IVTD  L   G A  +   L+   + + ++   + +PT   V
Sbjct: 466 SLPIALDEVITDGHKRAMIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSVV 525

Query: 78  AAGLKLLKENNCDSVISLGGGSPHDCAKGIALV-----------AANGGDIRD--YEGVD 124
             G +L+     D +I+LGGGSP D AK + ++           A    DIR   Y+   
Sbjct: 526 RKGAELMNSFKPDVIIALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPK 585

Query: 125 RSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMP 184
              K +  MIA+ TT+GT SE+T F ++TD+    K  + D  +TP +++ D++L++ MP
Sbjct: 586 MGVKAK--MIAVTTTSGTGSEVTPFAVVTDDETGQKYPLADYALTPDMAIVDANLVMDMP 643

Query: 185 KSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGS-NAKAREAM 243
           KSL A  G+DA+THA+EAYVS+ A+  +D  AL+A+ ++ ENLP +  +GS N  ARE +
Sbjct: 644 KSLCAFGGLDAVTHALEAYVSVLASEFSDGQALQALKLLKENLPASYHEGSKNPVARERV 703

Query: 244 AYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSK--------- 294
             A  +AG+AF NA LG  H+MAH+LG  +++PHG+ NA+L+ +V  +N+          
Sbjct: 704 HSAATIAGIAFANAFLGVCHSMAHKLGSQFHIPHGLANALLISNVIRYNANDNPTKQTAF 763

Query: 295 ------VAAARLRDCAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEE 348
                  A  R  + A  +G++  G   A   E  +  +  +  ++ IP  +R+  V+E 
Sbjct: 764 SQYDRPQARRRYAEVADHLGLSAPGDRTAAKIEKLLAWLESIKAELGIPKSIREAGVQEA 823

Query: 349 DFAV----LATNALKDACGFTNP 367
           DF      L+ +A  D C   NP
Sbjct: 824 DFLANVDKLSEDAFDDQCTGANP 846


Lambda     K      H
   0.318    0.131    0.373 

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: 693
Number of extensions: 26
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: 383
Length of database: 892
Length adjustment: 36
Effective length of query: 347
Effective length of database: 856
Effective search space:   297032
Effective search space used:   297032
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 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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