GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Dyella japonica UNC79MFTsu3.2

Align fumarylacetoacetate (FAA) hydrolase (EC 3.7.1.2) (characterized)
to candidate N515DRAFT_0362 N515DRAFT_0362 fumarylacetoacetate (FAA) hydrolase

Query= reanno::psRCH2:GFF3447
         (327 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0362
          Length = 328

 Score =  392 bits (1007), Expect = e-114
 Identities = 195/323 (60%), Positives = 244/323 (75%), Gaps = 1/323 (0%)

Query: 1   MKLATLNQG-RDGVLVVVSRDLAQAVKVPQIAATLQAALDDWNYCKPKLEAVYQRLNDGL 59
           MKL +L +G RDG L+VVSRDL++AVK   IAATLQAALDDW+   P+L A+Y  L  G 
Sbjct: 1   MKLGSLKEGGRDGTLIVVSRDLSRAVKATGIAATLQAALDDWSNLAPRLNALYGELQAGT 60

Query: 60  EEGAFAFDQTACHSPLPRAYHWADGSAYVNHVELVRKARGAEMPESFWHDPLMYQGGADA 119
              AFA D  A  +PLPRAY + DGSAY+ HVE VR+ARGAE+PESF+ DPLMYQ  +  
Sbjct: 61  APDAFALDVAAMAAPLPRAYEFVDGSAYLPHVERVRRARGAEVPESFYVDPLMYQATSAG 120

Query: 120 FIPPHSPIRLADEAWGIDLEGELAVITDDVPMGATPAEAASHIQLLMLVNDVSLRNLIPG 179
           F+ P  P+ +  E +GIDLE E+ VITDDVPM ATPA+A++HIQL+ LVNDVSLR LIP 
Sbjct: 121 FLAPRDPVLVPSEDYGIDLEAEVVVITDDVPMAATPAQASAHIQLVGLVNDVSLRGLIPA 180

Query: 180 ELAKGFGFYQSKPSSSFSPVAVTPDELGETWRDGKVHRPLVSHINGELFGQPDAGTDMTF 239
           ELAKGFGF QSKP S+ SPV VTPDELG+ WR+ K+H P+ + ING  FG+ + G DM F
Sbjct: 181 ELAKGFGFLQSKPRSALSPVFVTPDELGDVWREDKLHLPMRTWINGAWFGEAECGVDMQF 240

Query: 240 NFPTLVAHAARTRPLGAGTIIGSGTVSNYDRSAGSSCLAEKRMLEVVEHGEAKTPFLKFG 299
           +F  LVAHAA+TRPL AGTI+GSGT++N D   G+SCLAE+R +E +  G+  TPFLK+G
Sbjct: 241 SFAQLVAHAAKTRPLTAGTIVGSGTIANEDTGKGASCLAEQRTVETLRDGQPSTPFLKYG 300

Query: 300 DRVRIEMFDAAGQSIFGAIDQQV 322
           D +RI++ D  G SIFGAI+Q++
Sbjct: 301 DVIRIDVTDGDGASIFGAIEQRI 323


Lambda     K      H
   0.318    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: 395
Number of extensions: 7
Number of successful extensions: 1
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: 327
Length of database: 328
Length adjustment: 28
Effective length of query: 299
Effective length of database: 300
Effective search space:    89700
Effective search space used:    89700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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