GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Phaeobacter inhibens BS107

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate GFF2304 PGA1_c23360 putative iron containing alcohol dehydrogenase

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



>FitnessBrowser__Phaeo:GFF2304
          Length = 381

 Score =  191 bits (485), Expect = 3e-53
 Identities = 120/376 (31%), Positives = 178/376 (47%), Gaps = 13/376 (3%)

Query: 9   PSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGT 68
           P+    GA  + +     A  G  + L+VTD  L  L +       LE   +   ++   
Sbjct: 10  PTAIKFGAGRIRELAEACATAGMKKPLLVTDKGLADLPVTQSTLDILEAAGLGRAMFCEV 69

Query: 69  QPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVD---- 124
            PNP  +N+ AG+   K  + D VI+ GGGS  D  K +A +      + D+E +     
Sbjct: 70  DPNPNEKNLEAGVAAYKAGDHDGVIAFGGGSGLDLGKMVAFMCGQNRPVWDFEDIGDWWT 129

Query: 125 -RSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGM 183
              A    P+IA+ TTAGT SE+ R  +ITD   H K  I    V P + + D  L +GM
Sbjct: 130 RADADAIAPIIAVPTTAGTGSEVGRASVITDSVTHQKKIIFHPKVLPTVVICDPELTVGM 189

Query: 184 PKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAM 243
           PK +TA TG+DA  H +EA+ S    P++   AL+ + ++ E LP A  DG++ +AR  M
Sbjct: 190 PKFITAGTGLDAFAHCVEAFSSPHYHPMSQGIALEGMRLVKEYLPRAYADGTDIEARAQM 249

Query: 244 AYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDC 303
             A  +   AF    LG +HAM+H +G  +N  HG  NAV +  V  FN+   A R +  
Sbjct: 250 MSAAAMGATAFQK-GLGAIHAMSHPIGALFNTHHGTTNAVCMLAVLAFNAPEIADRFKTA 308

Query: 304 AAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACG 363
           A  +G++        G E     ++EL   + IP GL +L V E     L   AL D   
Sbjct: 309 ADYLGID-------GGFEGVCAYVQELNDSLGIPRGLSELGVTEAAIPELVKGALIDPSC 361

Query: 364 FTNPIQATHEEIVAIY 379
             NP+      +  ++
Sbjct: 362 GGNPVVLDQANLTQLF 377


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: 386
Number of extensions: 23
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: 381
Length adjustment: 30
Effective length of query: 353
Effective length of database: 351
Effective search space:   123903
Effective search space used:   123903
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 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