GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Herbaspirillum seropedicae SmR1

Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate HSERO_RS04630 HSERO_RS04630 3-hydroxy-2-methylbutyryl-CoA dehydrogenase

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



>FitnessBrowser__HerbieS:HSERO_RS04630
          Length = 254

 Score =  303 bits (776), Expect = 2e-87
 Identities = 155/248 (62%), Positives = 191/248 (77%), Gaps = 1/248 (0%)

Query: 8   FIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARELGDNARFAVADISDEQAAQ 67
           ++V+GAASGLGAATA+ L+ AGAKV+L D+N  A E     LG NARF + D++ E +AQ
Sbjct: 8   YVVTGAASGLGAATAEQLIRAGAKVVLADVNPVAGEKMQATLGANARFVLTDVTSETSAQ 67

Query: 68  SAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSFNLLRLAAA 127
                A S+ G++ GLVNCAGI   EK+LGK G H L SF + +N+NL+GSFN+ RLAA 
Sbjct: 68  EVFGVA-SSMGAVVGLVNCAGIAPGEKLLGKGGVHRLDSFMRALNINLVGSFNMARLAAQ 126

Query: 128 AMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELARFGIRVM 187
            ++ G AD +GERGVII+TASIAA+DGQ+GQ AYAASKG + S+TLP ARELAR GIRV+
Sbjct: 127 HISAGPADATGERGVIIHTASIAAFDGQMGQVAYAASKGGVVSMTLPMARELARHGIRVV 186

Query: 188 TIAPGIFETPMMAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHIIENSMLNGEVIRLD 247
           TIAPGI ETPMM GM +EV  SL+  VPFPPRLG+P E+A L  HI+EN  LNGEVIR+D
Sbjct: 187 TIAPGIIETPMMLGMPEEVLESLSRNVPFPPRLGKPSEFAGLVMHILENRYLNGEVIRMD 246

Query: 248 GALRMAAK 255
           GALRM+AK
Sbjct: 247 GALRMSAK 254


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: 196
Number of extensions: 7
Number of successful extensions: 2
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: 254
Length adjustment: 24
Effective length of query: 231
Effective length of database: 230
Effective search space:    53130
Effective search space used:    53130
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.

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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