GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Pseudomonas stutzeri RCH2

Align BadH (characterized)
to candidate GFF1114 Psest_1147 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

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



>FitnessBrowser__psRCH2:GFF1114
          Length = 252

 Score =  143 bits (360), Expect = 4e-39
 Identities = 92/260 (35%), Positives = 142/260 (54%), Gaps = 18/260 (6%)

Query: 3   RLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRC 62
           +LQ+K  ++TGGG G+G A     A +GA++A+ DLN +  ++   A + AGG A A  C
Sbjct: 2   QLQDKVIIVTGGGQGLGRAMGEYLAGKGARLALVDLNQERLDEAVAACKAAGGDARAYLC 61

Query: 63  DIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGE--------WERLIAIN 114
           ++A+   V   +A      G +  LVNNAG        K + GE        W+ +I +N
Sbjct: 62  NVANEEQVTDMVARVAEDFGGLHGLVNNAGILRDGLLLKVKDGEISKMSLAQWQAVIDVN 121

Query: 115 LTGALHMHHAVLPGMVE-RRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREH 173
           LTG       V   MVE +  G I+NI+S  +R G+ G+  Y+A K G+ + +   A+E 
Sbjct: 122 LTGVFLCTREVAAKMVELKSEGAIINISS-ISRAGNMGQTNYSAAKAGVASATVVWAKEL 180

Query: 174 ARHGITVNVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFG 233
           AR+GI V  V PG  +T ++A +      PE L E  T  IPL R+GKP ++A ++A+  
Sbjct: 181 ARYGIRVAGVAPGFIETEMVASM-----KPEAL-EKMTSGIPLKRMGKPAEIAHSVAYIF 234

Query: 234 SDDAGFITGQVLSVSGGLTM 253
            +D  + TG++L + GGL +
Sbjct: 235 END--YYTGRILELDGGLRL 252


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: 157
Number of extensions: 5
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: 252
Length adjustment: 24
Effective length of query: 231
Effective length of database: 228
Effective search space:    52668
Effective search space used:    52668
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