GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Phyllobacterium brassicacearum STM 196

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_106714455.1 CU102_RS29015 iron-containing alcohol dehydrogenase

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



>NCBI__GCF_003010955.1:WP_106714455.1
          Length = 388

 Score =  199 bits (507), Expect = 8e-56
 Identities = 120/381 (31%), Positives = 195/381 (51%), Gaps = 11/381 (2%)

Query: 9   PSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGT 68
           P+    GA  + +   ++   G  + L VTD  L KL +     K L++  +   ++   
Sbjct: 11  PTTVRFGAGRIKELPEVLEATGIKKPLFVTDPGLAKLPVVASTLKILDDAKVPYGVFSDV 70

Query: 69  QPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVD---- 124
           +PNP   N+ AG+ + K+   D VI+ GGGS  D  K IA  A     + D+E V     
Sbjct: 71  KPNPVDSNLTAGIAVFKKGKHDGVIAFGGGSALDLGKLIAFQAGQTRPVWDFEDVGDWWK 130

Query: 125 -RSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGM 183
             ++    P+IA+ TTAGT SE+ R  +IT+E  H K  I    + P + + D  L +GM
Sbjct: 131 RANSNAIAPIIAVPTTAGTGSEVGRAGVITNEETHTKKVIFHPKLLPAVVIADPELSVGM 190

Query: 184 PKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAM 243
           P  +TA TGMDAL H +EAY +    P+ D  A++ + ++ ENLP A  +G +  AR  M
Sbjct: 191 PAFITAGTGMDALAHCLEAYCAPGYHPMADGIAVEGIRLVFENLPKAYANGKDLTARAHM 250

Query: 244 AYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDC 303
             A  +   AF    LG +H+++H +G  Y+  HG+ NAV +P+V  FN +    R+   
Sbjct: 251 MSAATMGAAAFQK-GLGAIHSLSHPIGALYDTHHGMTNAVFMPYVLAFNREAVDERIARL 309

Query: 304 AAAMGVNVTGKNDAEG-AEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDAC 362
           A+ +G+    K    G A+A I   +EL     +P  ++DL++ ++   ++A  A+ D  
Sbjct: 310 ASYIGI----KGGFNGFAKAVIKLRKELKVPHTLPGLIKDLDMTKKQKELIADMAIVDPT 365

Query: 363 GFTNPIQATHEEIVAIYRAAM 383
              NP++ T +  + +   A+
Sbjct: 366 AGGNPVKLTKKAALKLLDEAI 386


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: 362
Number of extensions: 20
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: 388
Length adjustment: 30
Effective length of query: 353
Effective length of database: 358
Effective search space:   126374
Effective search space used:   126374
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