GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Sphingomonas koreensis DSMZ 15582

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate Ga0059261_2636 Ga0059261_2636 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway)

Query= BRENDA::A0A076VF18
         (308 letters)



>FitnessBrowser__Korea:Ga0059261_2636
          Length = 284

 Score =  120 bits (301), Expect = 4e-32
 Identities = 76/209 (36%), Positives = 113/209 (54%), Gaps = 19/209 (9%)

Query: 83  MGLQYSGDPAN---PQDKPPVACLFFKASQALAGPGDDIVLPRLARDEKNDYEVELCVVL 139
           +GL Y+   A    P  + PV  +F K    + GP D + +P+ ++  K D+EVEL +V+
Sbjct: 76  IGLNYADHAAESNLPIPEEPV--VFNKWVSCIQGPNDPVTIPKDSK--KTDWEVELGIVI 131

Query: 140 GKDAKDVDEKDAMSFVGGYCVVNDVSSR-GLCAKGGQWGMGKSYDTWCPFGPCLVSPSAL 198
           G  A +V E DA+  V GYCVVNDVS R     +G  W  GK + T+ P GP +V+   +
Sbjct: 132 GTAAHNVSEADALDHVAGYCVVNDVSERHWQTERGMTWDKGKGFPTFGPIGPWMVTADEV 191

Query: 199 GADPHKLTITTHVNGKLAQKGNTADLVLKIPELIARLSHGTTLQAGSLILTGSPIALGRK 258
           G DP  L++   VNGK  Q GNT  ++  + ++++ LS   TL  G +I TG+P      
Sbjct: 192 G-DPQNLSMWLSVNGKKVQDGNTRTMIFTVAQIVSYLSQIMTLLPGDVITTGTP------ 244

Query: 259 APGDAVEQSP---FMKDGDEIRCFVEGCG 284
            PG  + Q P   ++K GD +   +E  G
Sbjct: 245 -PGVGLGQKPEPWYLKAGDVVELGIEKLG 272


Lambda     K      H
   0.316    0.135    0.411 

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: 265
Number of extensions: 11
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: 308
Length of database: 284
Length adjustment: 26
Effective length of query: 282
Effective length of database: 258
Effective search space:    72756
Effective search space used:    72756
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: 48 (23.1 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