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_038858435.1 AFK65_RS00460 L-threonine dehydrogenase

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



>NCBI__GCF_001277175.1:WP_038858435.1
          Length = 383

 Score =  585 bits (1509), Expect = e-172
 Identities = 284/383 (74%), Positives = 332/383 (86%)

Query: 1   MAASTFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNI 60
           M AS F+IP++N+IG +SL +A+    +YG+   LIVTD ML+ LGMAG +++ L ++ I
Sbjct: 1   MTASVFYIPAINMIGMNSLDEALKTACEYGYRNALIVTDGMLSALGMAGQLKEMLAQKGI 60

Query: 61  FSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDY 120
            SV++DGT PNPTTENV AGL +L+ + CD VISLGGGSPHDCAKGIALVAANGGDIRDY
Sbjct: 61  HSVVFDGTHPNPTTENVEAGLSMLRAHRCDCVISLGGGSPHDCAKGIALVAANGGDIRDY 120

Query: 121 EGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLM 180
           EGVDRS KPQLPMIAINTTAGTASEMTRFCIITD+ RH+KMAIVDKHVTP++SVND +LM
Sbjct: 121 EGVDRSRKPQLPMIAINTTAGTASEMTRFCIITDQERHVKMAIVDKHVTPVMSVNDPALM 180

Query: 181 IGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAR 240
           +GMPKSLTAATGMDALTHAIEAYVS AATP+TDACALKA+ MIA+ LP AVE+G N  AR
Sbjct: 181 MGMPKSLTAATGMDALTHAIEAYVSTAATPVTDACALKAIAMIAQTLPQAVEEGDNVAAR 240

Query: 241 EAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARL 300
           EAMA+AQF+AGMAFNNASLGYVHAMAHQLGGFY+LPHGVCNA+LLPHVQ FNS  A  RL
Sbjct: 241 EAMAWAQFMAGMAFNNASLGYVHAMAHQLGGFYDLPHGVCNAILLPHVQRFNSAAAGHRL 300

Query: 301 RDCAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKD 360
           RDCA AMGV+V+G +DAEGA ACI AI  LA+++ IPAGLR+L V+E+D + LA NALKD
Sbjct: 301 RDCAQAMGVDVSGMSDAEGANACIAAICALARRIHIPAGLRELRVREDDISELAENALKD 360

Query: 361 ACGFTNPIQATHEEIVAIYRAAM 383
           ACGFTNP+QA+H EI+AIYRAA+
Sbjct: 361 ACGFTNPVQASHAEIMAIYRAAL 383


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: 570
Number of extensions: 17
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: 383
Length of database: 383
Length adjustment: 30
Effective length of query: 353
Effective length of database: 353
Effective search space:   124609
Effective search space used:   124609
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: 50 (23.9 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