GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Rhodococcus qingshengii djl-6-2

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate WP_050656959.1 C1M55_RS12530 fumarylacetoacetate hydrolase family protein

Query= BRENDA::A0A076VF18
         (308 letters)



>NCBI__GCF_002893965.1:WP_050656959.1
          Length = 257

 Score =  120 bits (301), Expect = 3e-32
 Identities = 85/253 (33%), Positives = 124/253 (49%), Gaps = 22/253 (8%)

Query: 39  ERITARVVAAPWTSSPASTSSPRVLTVQTLLSPLAPTDVPAIRGMGLQYSGDPANPQDKP 98
           + + A+ +A     +P  T     L    LL+P+  + V  I   G  Y+   A    + 
Sbjct: 22  DALVAKEIAEHPFGNPTFTGRSWPLADVRLLAPILASKVICI---GKNYADHIAEMGGEA 78

Query: 99  PV-ACLFFKASQALAGPGDDIVLPRLARDEKNDYEVELCVVLGKDAKDVDEKDAMSFVGG 157
           P    +F K + ++ GPG  IVLP  + +    +E EL VV+G+  KDV    A+S V G
Sbjct: 79  PADPVIFLKPNTSIVGPGAPIVLPPTSNEVH--FEGELAVVIGQPCKDVPAAKALSVVLG 136

Query: 158 YCVVNDVSSRGLCAKGGQWGMGKSYDTWCPFGPCLVSPSALGADPHKLTITTHVNGKLAQ 217
           Y + NDVS+R      GQW   K +DT+CP GP + +      D   + I T VNG++ Q
Sbjct: 137 YTIANDVSARDHQRHDGQWTRAKGHDTFCPLGPWIET----SLDASDVDIRTEVNGQVKQ 192

Query: 218 KGNTADLVLKIPELIARLSHGTTLQAGSLILTGSPIALGRKAPGDAVEQSPFMKDGDEIR 277
             +TA L+  IP++I  +S   TL  G +ILTG+P  +G             + DGD + 
Sbjct: 193 DSSTAFLLHDIPKIIEWISAVMTLLPGDVILTGTPAGVGP------------IVDGDSVS 240

Query: 278 CFVEGCGTLINSV 290
             V G GTL N V
Sbjct: 241 VTVSGIGTLTNPV 253


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: 251
Number of extensions: 18
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: 257
Length adjustment: 26
Effective length of query: 282
Effective length of database: 231
Effective search space:    65142
Effective search space used:    65142
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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