GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HDOP-hydrol in Klebsiella michiganensis M5al

Align FAA hydrolase family protein (characterized, see rationale)
to candidate BWI76_RS03870 BWI76_RS03870 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase

Query= uniprot:A0A2E7P912
         (281 letters)



>FitnessBrowser__Koxy:BWI76_RS03870
          Length = 254

 Score =  143 bits (361), Expect = 3e-39
 Identities = 78/196 (39%), Positives = 111/196 (56%)

Query: 71  GKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKKTDWEVELGVV 130
           G    +GLNYADHA+E     P EP+VF K  +  +G   +   P   +   +E EL VV
Sbjct: 44  GTLFALGLNYADHASELAFTPPTEPLVFIKAPNTFIGHRQESVRPDNVEYMHYEAELVVV 103

Query: 131 IGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGPIGPWLVTRDE 190
           IGK    + E DAM++VAGY V ND + R+Y         + K  DT  PIGPW+V ++ 
Sbjct: 104 IGKTARKVAEADAMAYVAGYTVCNDYAIRDYLENYYRPNLRVKSRDTLTPIGPWIVGKEA 163

Query: 191 VADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTPPGVGMG 250
           + DP  L +   V+G+  Q G T+ +IF +  +++YLS FM+LQPGD+I+TGTP G+   
Sbjct: 164 IPDPHNLALCTWVNGELRQQGTTADLIFSIPFLIAYLSEFMTLQPGDMIATGTPKGLSDV 223

Query: 251 VKPEAVYLRAGQTMRL 266
           V  + V +      RL
Sbjct: 224 VPGDEVIVEVEGVGRL 239


Lambda     K      H
   0.316    0.138    0.419 

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: 201
Number of extensions: 3
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: 281
Length of database: 254
Length adjustment: 25
Effective length of query: 256
Effective length of database: 229
Effective search space:    58624
Effective search space used:    58624
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: 42 (22.0 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