GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Burkholderia phytofirmans PsJN

Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate BPHYT_RS25360 BPHYT_RS25360 enoyl-CoA hydratase

Query= metacyc::MONOMER-15953
         (257 letters)



>FitnessBrowser__BFirm:BPHYT_RS25360
          Length = 256

 Score =  154 bits (389), Expect = 2e-42
 Identities = 93/242 (38%), Positives = 130/242 (53%), Gaps = 2/242 (0%)

Query: 17  ITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKEMAERDLV 76
           +TL RP A+N+LN ++   L A+L     D   R +V+TG+ +AF AGAD+ E AE    
Sbjct: 14  LTLDRPAAMNSLNREMATGLIAQLKAWRNDDAVRVLVVTGNGRAFCAGADLIEAAEATQP 73

Query: 77  GILE--DPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARFGQPEINL 134
           G  E  +  V  +  + AF KP+IAAVNG  L GG E+ +  D+++A E AR G    N 
Sbjct: 74  GRREFLELIVEFFDTLRAFPKPVIAAVNGLALAGGLEVVLACDVVLAAESARLGDAHSNF 133

Query: 135 GIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTIERALAIAR 194
           G+ PGAGG   L R V  ++A  ++ +G A+ A   +  GLV+EV        RA A+A 
Sbjct: 134 GVFPGAGGAAILPRKVPANVARYLLFTGDAMSAAELKGYGLVNEVLADAELRPRAQALAH 193

Query: 195 VIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRAEGIRAFQEKRRPEF 254
             A+K+PL +   K    +  D   A  LR E         + D  EG+RAF EKR P+F
Sbjct: 194 KFAKKSPLVLARMKRVANETADKSAADALRHELLELRNHQRSYDVQEGLRAFAEKREPQF 253

Query: 255 TG 256
            G
Sbjct: 254 KG 255


Lambda     K      H
   0.320    0.134    0.374 

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: 158
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: 257
Length of database: 256
Length adjustment: 24
Effective length of query: 233
Effective length of database: 232
Effective search space:    54056
Effective search space used:    54056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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