GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Phaeobacter inhibens BS107

Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate GFF3147 PGA1_c31980 short chain dehydrogenase

Query= metacyc::MONOMER-11802
         (255 letters)



>FitnessBrowser__Phaeo:GFF3147
          Length = 253

 Score = 98.6 bits (244), Expect = 1e-25
 Identities = 82/259 (31%), Positives = 118/259 (45%), Gaps = 21/259 (8%)

Query: 1   MHIANKHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKAREL-----GDNARF 55
           M +A K  IV+G ASG GA      +  GA+VM+ D+NA A  A A ++      D A  
Sbjct: 1   MRLAGKCAIVTGGASGFGAGIVTKFLTEGARVMIADINADAAAAAASDVCETYGPDRAIA 60

Query: 56  AVADISDEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNL 115
              D+SD  +      AA++ FG +  LVN AG+      L          F +V+ VN+
Sbjct: 61  QTVDVSDRASVDQMAQAALNHFGQIDILVNNAGVSHLPTPLEDVSEE---DFDRVVAVNM 117

Query: 116 IGSFNLLRLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPA 175
              +   R     M      +S + G I+N AS A    +     Y ASKG + + T   
Sbjct: 118 KSVYLTARALVPHM------KSRQSGAILNVASTAGVSPRPNLNWYNASKGWMITATRTM 171

Query: 176 ARELARFGIRVMTIAPGIFETPM----MAGMSDEVRASLAAGVPFPPRLGRPQEYAALAR 231
           A ELA  G+RV  I P   ETP+    M   + EVRA   + +P   R   P++    A 
Sbjct: 172 AVELAPAGVRVNAINPVAGETPLLKTFMGEDTPEVRAKFLSTIPI-GRFSTPEDMGNAAC 230

Query: 232 HII--ENSMLNGEVIRLDG 248
           ++   E SM+ G  + +DG
Sbjct: 231 YLCSDEASMVTGVALEVDG 249


Lambda     K      H
   0.318    0.131    0.358 

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: 120
Number of extensions: 6
Number of successful extensions: 3
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: 255
Length of database: 253
Length adjustment: 24
Effective length of query: 231
Effective length of database: 229
Effective search space:    52899
Effective search space used:    52899
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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