GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpE in Klebsiella michiganensis M5al

Align 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase; 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; HHED aldolase; 4-hydroxy-2-ketoheptane-1,7-dioate aldolase; HKHD aldolase; EC 4.1.2.52 (characterized)
to candidate BWI76_RS19980 BWI76_RS19980 2-keto-3-deoxy-L-rhamnonate aldolase

Query= SwissProt::Q47098
         (262 letters)



>FitnessBrowser__Koxy:BWI76_RS19980
          Length = 267

 Score =  294 bits (752), Expect = 1e-84
 Identities = 143/250 (57%), Positives = 185/250 (74%)

Query: 1   MENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAI 60
           + N FKA L  G  QIGLWL  +SSY AE+ A +G+DWLLIDGEHAPN +Q +  QLQAI
Sbjct: 5   LSNPFKAGLLQGEAQIGLWLSSTSSYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAI 64

Query: 61  APYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGS 120
           APY SQPV+RP   +   IKQ+LD+G +TLL+PMV  A++ARE V ATRYPP G RGVG+
Sbjct: 65  APYVSQPVIRPVEGNRSLIKQVLDIGARTLLIPMVDTAEQAREIVSATRYPPVGTRGVGA 124

Query: 121 ALARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADM 180
            +ARA+RW R+ +Y+ +AND++C+L+Q+E++ A+ NL  IL+VEG+DGVFIGPADLSA +
Sbjct: 125 GVARAARWGRVENYMAQANDELCLLIQVESKTALDNLDAILEVEGIDGVFIGPADLSASL 184

Query: 181 GYAGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLA 240
           GY  N  HP+VQ  IEQ+I +IR +GKA G L  + ++A + L  GA FVAVGVDT L  
Sbjct: 185 GYPDNAGHPDVQRIIEQSIRRIRAAGKAAGFLAVDPEMAHKALAWGANFVAVGVDTNLYT 244

Query: 241 RAAEALAARF 250
           RA +   A F
Sbjct: 245 RALDKRLAMF 254


Lambda     K      H
   0.317    0.133    0.387 

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: 216
Number of extensions: 7
Number of successful extensions: 1
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: 262
Length of database: 267
Length adjustment: 25
Effective length of query: 237
Effective length of database: 242
Effective search space:    57354
Effective search space used:    57354
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 (21.7 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