GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpD in Cupriavidus basilensis 4G11

Align 2-keto-4-pentenoate hydratase; 2-hydroxypentadienoic acid hydratase; EC 4.2.1.80 (characterized)
to candidate RR42_RS27885 RR42_RS27885 2-keto-4-pentenoate hydratase

Query= SwissProt::Q9S156
         (260 letters)



>FitnessBrowser__Cup4G11:RR42_RS27885
          Length = 258

 Score =  342 bits (878), Expect = 4e-99
 Identities = 177/252 (70%), Positives = 206/252 (81%), Gaps = 2/252 (0%)

Query: 9   AWAERLRHAEATATPIAPLREEITDNDSA--YAVQLVNVQYAQSQGRRIVGRKIGLTSLA 66
           A A RLR AE T TP+ PLR EI   D+A  YA+Q  NV   ++QGRR+ GRKIGLTS A
Sbjct: 4   ALARRLREAEQTRTPVEPLRGEIPPGDAAMAYAIQRANVDAWRAQGRRVAGRKIGLTSPA 63

Query: 67  VQKQLGVDQPDFGTLFADMLYGDDEAVPLSRTLQPKVEAEVALVLAKDLERPDTTLVDVI 126
           VQ+QLGVDQPDFGTLFADM++GDDE +P++RTLQPK EAEVALVL +D+ + D TLVD+I
Sbjct: 64  VQRQLGVDQPDFGTLFADMVFGDDEPIPVARTLQPKAEAEVALVLCRDVPQKDATLVDLI 123

Query: 127 SATAYVLPAIEIVGSRIADWNIRFIDTVADNASSGLVVLGAVPTALNALDLKLCQMQMTR 186
           +A AYVLPAIE+VGSRI +W+I ++DTVADNASSGLVVLGAVP  L  LDLK  +M+M R
Sbjct: 124 NAVAYVLPAIEVVGSRIRNWDISYVDTVADNASSGLVVLGAVPVPLAGLDLKTVKMEMLR 183

Query: 187 NGDVVSTGSGGACLGHPLNAAVWLARRLANLGQPLRAGDLVLTGALGPMVAVNAGDRFEA 246
           + + VSTGSG  CLGHPLNAAVWLAR+LA LG PLRAGDL+LTGALGPMVAV  G  FEA
Sbjct: 184 DDERVSTGSGADCLGHPLNAAVWLARKLAALGDPLRAGDLILTGALGPMVAVAPGQCFEA 243

Query: 247 RISGIGSVCAQF 258
           RISGIGSV A+F
Sbjct: 244 RISGIGSVRARF 255


Lambda     K      H
   0.319    0.134    0.386 

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: 270
Number of extensions: 12
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: 260
Length of database: 258
Length adjustment: 24
Effective length of query: 236
Effective length of database: 234
Effective search space:    55224
Effective search space used:    55224
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 (21.7 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