GapMind for catabolism of small carbon sources

 

Alignments for a candidate for KDF-hydrolase in Azospirillum brasilense Sp245

Align 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-) (characterized)
to candidate AZOBR_RS15905 AZOBR_RS15905 2-hydroxyhepta-2 4-diene-1 7-dioate isomerase

Query= reanno::BFirm:BPHYT_RS34210
         (282 letters)



>FitnessBrowser__azobra:AZOBR_RS15905
          Length = 283

 Score =  358 bits (920), Expect = e-104
 Identities = 172/282 (60%), Positives = 215/282 (76%)

Query: 1   MKLLRYGPKGQEKPGLLDAQGKIRDLSKVVADIDGAALTDEGLAKLRALDPASLPLVEGN 60
           MKLLR+GP G E+PGLLD  G IRDLS VV+DI  + LT++GLA LR LD   L  V   
Sbjct: 1   MKLLRFGPPGHERPGLLDRNGVIRDLSGVVSDIGPSTLTEDGLAHLRTLDTDRLAQVPDG 60

Query: 61  PRMGPCVGKIGKFICIGLNYADHAAESNLPVPAEPVIFNKWTSAISGPNDDVEIPRGSKK 120
            R+GPCV  + K +C+GLNY  HAAES LP PAEPV+F K T++I GPND V++PRG+ K
Sbjct: 61  TRLGPCVTGVSKVVCVGLNYRAHAAESGLPEPAEPVLFMKATTSICGPNDPVQMPRGATK 120

Query: 121 TDWEVELGVVIGKPAKYIDEANALDYVAGYCVINDVSEREWQIEKGGTWDKGKGFDTFGP 180
            DWEVELG+VIG+ A+Y+++A+A D++AGYCV+NDVSER +Q E  G W KGK  D+F P
Sbjct: 121 LDWEVELGIVIGRTARYVEQADAFDHIAGYCVLNDVSERAFQTESTGQWVKGKSADSFCP 180

Query: 181 IGPWVVTRDEVADPQNLSLWLEVDGHRYQNGSTKTMVFGVAKLVSYVSQCMSLQPGDVIS 240
           IGPW+VTRDEV DPQ L LWLEVDG   Q+ +T  M+FGVA++VSY+S+ M+L PGDVI+
Sbjct: 181 IGPWMVTRDEVPDPQALRLWLEVDGQPMQDSTTADMIFGVAEIVSYISRFMTLLPGDVIA 240

Query: 241 TGTPPGVGMGVKPNPVFLKPGQTIRLGIEGLGEQTQKTYAAE 282
           TGTP GV +G  PN  +L+PGQT+RLG+EGLGEQ Q   A E
Sbjct: 241 TGTPQGVALGRGPNHPWLQPGQTMRLGVEGLGEQRQSVRAFE 282


Lambda     K      H
   0.315    0.138    0.422 

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: 368
Number of extensions: 10
Number of successful extensions: 1
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: 282
Length of database: 283
Length adjustment: 26
Effective length of query: 256
Effective length of database: 257
Effective search space:    65792
Effective search space used:    65792
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: 42 (21.9 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