GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Erythrobacter gangjinensis K7-2

Align BadH (characterized)
to candidate WP_047007388.1 AAW01_RS11455 SDR family oxidoreductase

Query= metacyc::MONOMER-893
         (255 letters)



>NCBI__GCF_001010925.1:WP_047007388.1
          Length = 266

 Score =  159 bits (403), Expect = 4e-44
 Identities = 98/266 (36%), Positives = 136/266 (51%), Gaps = 12/266 (4%)

Query: 1   MARLQNKTAVITGGGG--GIGGATCRRFAQEGAKIAVFDLNLD-AAEKVAGAIRDAGGTA 57
           M R   KT V+TG G   G+G    + FA EGA   V D+ LD   + VA  +R  G   
Sbjct: 1   MGRFTGKTIVVTGSGKEKGLGQGILQAFADEGANCVVSDVRLDDEVDGVADELRQRGAKV 60

Query: 58  EAVRCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDI-FKPFTKTEPG-EWERLIAINL 115
             V+CD++D  S  A +A      G VD+ VNNAG     KP    +   EW++++A+NL
Sbjct: 61  ATVQCDVSDAASCQALVAQALDHFGSVDVFVNNAGIGFKMKPLLDVDTADEWDQVLAVNL 120

Query: 116 TGALHMHHAVLPGMVER-RHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHA 174
           +GA +   A    MV+  + GRI+NIAS AA+ G      Y + K G+V  ++  A E  
Sbjct: 121 SGAFYCTQAAARAMVDAGKGGRIINIASQAAKTGFPHLPAYVSSKHGMVGLTRASAVELG 180

Query: 175 RHGITVNVVCPGPTDTALLADVTS------GAANPEKLIEAFTKAIPLGRLGKPDDLAGA 228
            HGITVN +CP    T L A          G A  E  +       P+GR G P D A A
Sbjct: 181 AHGITVNAICPNHVTTGLGAQQNEYFSKLLGFAKVEDYLANMAAKNPMGRPGLPSDTAAA 240

Query: 229 IAFFGSDDAGFITGQVLSVSGGLTMN 254
             +  SD+A ++TG+ L++SGG  M+
Sbjct: 241 CLWLASDEAVYVTGEALNISGGEEMH 266


Lambda     K      H
   0.318    0.135    0.398 

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: 198
Number of extensions: 13
Number of successful extensions: 5
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: 266
Length adjustment: 24
Effective length of query: 231
Effective length of database: 242
Effective search space:    55902
Effective search space used:    55902
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 24 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