GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Paraburkholderia bryophila 376MFSha3.1

Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate H281DRAFT_03491 H281DRAFT_03491 short chain enoyl-CoA hydratase (EC 4.2.1.17)/Enoyl-CoA hydratase (EC 4.2.1.17)

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



>FitnessBrowser__Burk376:H281DRAFT_03491
          Length = 266

 Score =  141 bits (356), Expect = 1e-38
 Identities = 101/256 (39%), Positives = 134/256 (52%), Gaps = 14/256 (5%)

Query: 13  GVRLITLQRPEALNALNT-QLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKEMA 71
           GV  ITL RPE  NAL   +++D L   L  A+ D   RA+VLTG+  AF++G +IK M 
Sbjct: 12  GVATITLNRPETRNALTEMEVVDALVESLERAQADLNVRAIVLTGAGPAFSSGGNIKHM- 70

Query: 72  ERDLVG--------ILEDPRVAHWQRIAAFSK---PLIAAVNGFCLGGGCELAMHADILI 120
            RD VG        I E+ R    +   AF +   P IAAVNG   G GC+LA+  DI I
Sbjct: 71  -RDEVGTFGGNSAQIRENYRRGIQRIPRAFHELDLPCIAAVNGPAHGAGCDLALMCDIRI 129

Query: 121 AGEDARFGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVT 180
           A   A F +    +GI+PG GG   L RAVG S A +M+ +G  IDA+ A   GLVS V 
Sbjct: 130 AAHSALFAESFAKIGIIPGDGGAWLLPRAVGLSRAAEMIFTGTPIDAQCALDWGLVSRVV 189

Query: 181 LPELTIERALAIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRA 240
                +  A  +A  IA   P  +R++K  + + +  DL S L        ++  TAD  
Sbjct: 190 PDAELLSTARELAARIASNPPNVLRMSKRLIREGQRMDLPSLLELSAAFQGIVHRTADHR 249

Query: 241 EGIRAFQEKRRPEFTG 256
           E + A  EKR P +TG
Sbjct: 250 EALAATFEKRTPNYTG 265


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: 175
Number of extensions: 12
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: 266
Length adjustment: 25
Effective length of query: 232
Effective length of database: 241
Effective search space:    55912
Effective search space used:    55912
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