GapMind for catabolism of small carbon sources

 

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

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (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= CharProtDB::CH_091794
         (261 letters)



>FitnessBrowser__Burk376:H281DRAFT_03491
          Length = 266

 Score =  161 bits (408), Expect = 1e-44
 Identities = 100/258 (38%), Positives = 150/258 (58%), Gaps = 13/258 (5%)

Query: 6   VILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIEN---DSEVLAVILTGAGEKSF 62
           V+ E +G VA +T+NRP+  NAL    ++ +D ++  +E    D  V A++LTGAG  +F
Sbjct: 5   VLYELDGGVATITLNRPETRNALTE--MEVVDALVESLERAQADLNVRAIVLTGAGP-AF 61

Query: 63  VAGADISEMK-EMNTIEGRKFGILGN------KVFRRLELLEKPVIAAVNGFALGGGCEI 115
            +G +I  M+ E+ T  G    I  N      ++ R    L+ P IAAVNG A G GC++
Sbjct: 62  SSGGNIKHMRDEVGTFGGNSAQIRENYRRGIQRIPRAFHELDLPCIAAVNGPAHGAGCDL 121

Query: 116 AMSCDIRIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALR 175
           A+ CDIRIA+ +A F +    +GI PG GG   L R VG+  A ++IFT   I A  AL 
Sbjct: 122 ALMCDIRIAAHSALFAESFAKIGIIPGDGGAWLLPRAVGLSRAAEMIFTGTPIDAQCALD 181

Query: 176 IGLVNKVVEPSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGE 235
            GLV++VV  +EL++TA+E+A +I SN P  +++SK+ I  G + D+ + L   +   G 
Sbjct: 182 WGLVSRVVPDAELLSTARELAARIASNPPNVLRMSKRLIREGQRMDLPSLLELSAAFQGI 241

Query: 236 CFSTEDQKDAMTAFIEKR 253
              T D ++A+ A  EKR
Sbjct: 242 VHRTADHREALAATFEKR 259


Lambda     K      H
   0.317    0.134    0.365 

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: 169
Number of extensions: 8
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: 261
Length of database: 266
Length adjustment: 25
Effective length of query: 236
Effective length of database: 241
Effective search space:    56876
Effective search space used:    56876
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 (21.6 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