GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Burkholderia phytofirmans PsJN

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

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>FitnessBrowser__BFirm:BPHYT_RS25360
          Length = 256

 Score =  148 bits (374), Expect = 1e-40
 Identities = 93/257 (36%), Positives = 141/257 (54%), Gaps = 4/257 (1%)

Query: 1   MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKA 60
           M+Y + +V++   VG +TL+RP A+N+LN  +   L A L+ +  DDA+  +VVTG+ +A
Sbjct: 1   MSYSHAVVDS---VGWLTLDRPAAMNSLNREMATGLIAQLKAWRNDDAVRVLVVTGNGRA 57

Query: 61  FAAGADIGMMSTYTYMDVYKG-DYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDI 119
           F AGAD+   +  T     +  + I   ++T+R+  KP+IAAV G AL GG E+ + CD+
Sbjct: 58  FCAGADLIEAAEATQPGRREFLELIVEFFDTLRAFPKPVIAAVNGLALAGGLEVVLACDV 117

Query: 120 IFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSR 179
           + AA++A+ G      G+ PGAGG   LPR V    A  L  T   M AAE +  GLV+ 
Sbjct: 118 VLAAESARLGDAHSNFGVFPGAGGAAILPRKVPANVARYLLFTGDAMSAAELKGYGLVNE 177

Query: 180 VIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATED 239
           V+  A L   A A A   A+     +  +K   N   + + A+ +  E     +   + D
Sbjct: 178 VLADAELRPRAQALAHKFAKKSPLVLARMKRVANETADKSAADALRHELLELRNHQRSYD 237

Query: 240 QKEGMAAFVEKRKPVFK 256
            +EG+ AF EKR+P FK
Sbjct: 238 VQEGLRAFAEKREPQFK 254


Lambda     K      H
   0.321    0.134    0.380 

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: 150
Number of extensions: 9
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: 258
Length of database: 256
Length adjustment: 24
Effective length of query: 234
Effective length of database: 232
Effective search space:    54288
Effective search space used:    54288
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 (21.9 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