GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Cupriavidus basilensis 4G11

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate RR42_RS00385 RR42_RS00385 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase

Query= BRENDA::A0A076VF18
         (308 letters)



>FitnessBrowser__Cup4G11:RR42_RS00385
          Length = 280

 Score =  146 bits (368), Expect = 6e-40
 Identities = 90/214 (42%), Positives = 121/214 (56%), Gaps = 14/214 (6%)

Query: 75  TDVPAIRGMGLQYSGDPANP-QDKPPVACLFFKASQALAGPGDDIVLPRLARDEKNDYEV 133
           T +  I  +GL Y+   A      P    +F KA+ +L GP D ++LPR    EK D+EV
Sbjct: 67  TGIGKIVAIGLNYADHAAEAGMALPAEPIVFLKANSSLNGPNDPVMLPR--GSEKTDWEV 124

Query: 134 ELCVVLGKDAKDVDEKDAMSFVGGYCVVNDVSSRGL-CAKGGQWGMGKSYDTWCPFGPCL 192
           EL VV+GK A+DV   DA+S V GYCVVNDVS R     +GG W  GK  DT+CP GP L
Sbjct: 125 ELGVVIGKVARDVSLADALSHVAGYCVVNDVSEREFQIERGGTWDKGKGCDTFCPVGPWL 184

Query: 193 VSPSALGADPHKLTITTHVNGKLAQKGNTADLVLKIPELIARLSHGTTLQAGSLILTGSP 252
           V+   +  DP  L +   VNG+  QKG+TA +V  +  L++ +S   TL  G LI TG+P
Sbjct: 185 VTRDEV-PDPQALGLWLDVNGQRVQKGSTATMVFDVATLVSYVSRFMTLHPGDLICTGTP 243

Query: 253 --IALGRKAPGDAVEQSPFMKDGDEIRCFVEGCG 284
             + +G K P        F+K GD +R  ++G G
Sbjct: 244 PGVGMGFKPP-------RFLKAGDTMRLGIDGLG 270


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: 286
Number of extensions: 16
Number of successful extensions: 4
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: 280
Length adjustment: 26
Effective length of query: 282
Effective length of database: 254
Effective search space:    71628
Effective search space used:    71628
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