GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fahA in Paraburkholderia bryophila 376MFSha3.1

Align fumarylacetoacetate hydrolase (EC 3.7.1.2) (characterized)
to candidate H281DRAFT_02070 H281DRAFT_02070 fumarylacetoacetate (FAA) hydrolase

Query= reanno::MR1:200835
         (328 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02070 H281DRAFT_02070
           fumarylacetoacetate (FAA) hydrolase
          Length = 327

 Score =  428 bits (1100), Expect = e-124
 Identities = 203/323 (62%), Positives = 252/323 (78%)

Query: 1   MKLASYNNGRRDGQLMLVSRDLTQTVAVPAIAHTMQQLLDGWELLKPQLQELYDALNEGK 60
           MKLA+  +G RDGQL++VSRDL       AIA T+Q++LD W    PQL +LYDALN+G+
Sbjct: 1   MKLATLKDGTRDGQLIVVSRDLHTAAVADAIAPTLQRVLDDWTFYAPQLHDLYDALNQGR 60

Query: 61  LPNTQTFDETKCLSPLPRAYQWADGSAYVNHVELVRKARGAEMPETFWTDPLFYQGGSDS 120
             NT +FD + C++PLPRA+QWADGS+YVNHVELVR+ARGAEMP  FWTDPL YQGGSD 
Sbjct: 61  ARNTFSFDASDCMAPLPRAFQWADGSSYVNHVELVRRARGAEMPPEFWTDPLMYQGGSDD 120

Query: 121 FIAPKADIPLASEDWGIDFESEIAVITDDVPMGVSAENAAKHIKLLMLVNDVSLRNLIPA 180
           FI P+ D+  ASE +GIDFE+E+AVIT DVPMG + E + K ++L+ LVNDVSLRNLIPA
Sbjct: 121 FIGPEDDVVCASEAFGIDFEAEVAVITTDVPMGATPEQSLKSVRLITLVNDVSLRNLIPA 180

Query: 181 ELAKGFGFFQSKPSSSFSPVAITPDELGHRWEDSKVHLPLITYLNGELFGRPNAGVDMTF 240
           ELAKGFGFFQSKP+SSF+PVA+TPDELG  W + +VH P+I + NG+  G+P+AG DM F
Sbjct: 181 ELAKGFGFFQSKPASSFAPVAVTPDELGEHWREGRVHRPMIVHWNGKKVGQPDAGTDMVF 240

Query: 241 NFSQLVSHVAKTRPLGAGAIIGSGTISNYDRSAGSSCLAEKRMLEVIADGKASTPFMRFG 300
           +F QL++H AKTR L AGAI+GSGT+SN D   G  C+AEKR LE I  G   T FM++G
Sbjct: 241 HFGQLIAHAAKTRNLRAGAIVGSGTVSNKDAKRGYCCIAEKRCLETIEHGAPQTEFMKYG 300

Query: 301 DTVRIEMLDDNGVSIFGSIDQKV 323
           DTV+IEM D+ G SIFGSI+Q +
Sbjct: 301 DTVKIEMFDEAGKSIFGSIEQSI 323


Lambda     K      H
   0.317    0.134    0.397 

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: 333
Number of extensions: 6
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: 328
Length of database: 327
Length adjustment: 28
Effective length of query: 300
Effective length of database: 299
Effective search space:    89700
Effective search space used:    89700
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 (21.7 bits)
S2: 48 (23.1 bits)

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

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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