GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Pseudomonas fluorescens FW300-N2E2

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate Pf6N2E2_229 Putative fumarylacetoacetate (FAA) hydrolase

Query= BRENDA::A0A076VF18
         (308 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_229
          Length = 283

 Score =  100 bits (250), Expect = 3e-26
 Identities = 77/244 (31%), Positives = 119/244 (48%), Gaps = 13/244 (5%)

Query: 53  SPASTSS-PRVLTVQTLLSPLAPTDVPAIRGMGLQYSGDPANP-QDKPPVACLFFKASQA 110
           SPA  +  PR+        P+ P     +  +G+ Y+       ++ P    +F + + +
Sbjct: 49  SPARLARLPRIPLADVTFLPVIPNPGKVLC-IGINYATHVRETGREMPTYPMIFTRFADS 107

Query: 111 LAGPGDDIVLPRLARDEKNDYEVELCVVLGKDAKDVDEKDAMSFVGGYCVVNDVSSRGLC 170
                  IV P  +   K D+E EL VV+GK A+ V   DA+ +V GY   ND S R   
Sbjct: 108 QTAHLQPIVRPTASH--KLDFEGELAVVIGKAARHVKHADALDYVAGYACYNDGSVRDWQ 165

Query: 171 AKGGQWGMGKSYDTWCPFGPCLVSPSALGADPHKLTITTHVNGKLAQKGNTADLVLKIPE 230
               Q+  GK++     FGP LV+   +G DP  L +TT +NG++ Q   T+D++  + +
Sbjct: 166 KHTIQFVPGKNFPNTGGFGPWLVTGDEIG-DPQDLELTTRLNGEVMQHTRTSDMIFDVRQ 224

Query: 231 LIARLSHGTTLQAGSLILTGSPIALGRKAPGDAVEQSP-FMKDGDEIRCFVEGCGTLINS 289
           LI   S  T L  G +I+TG+   +G      A  + P +MK GDE+   +   GTL NS
Sbjct: 225 LIEYCSTFTELAPGDVIVTGTTGGVG------AFREPPVWMKPGDEVEIEIARIGTLRNS 278

Query: 290 VRDE 293
           + DE
Sbjct: 279 IVDE 282


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: 253
Number of extensions: 12
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: 283
Length adjustment: 26
Effective length of query: 282
Effective length of database: 257
Effective search space:    72474
Effective search space used:    72474
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