GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Acidovorax sp. GW101-3H11

Align fumarylacetoacetate hydrolase (EC 3.7.1.2) (characterized)
to candidate Ac3H11_4507 Fumarylacetoacetate hydrolase family protein

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_4507
          Length = 337

 Score =  390 bits (1001), Expect = e-113
 Identities = 195/332 (58%), Positives = 246/332 (74%), Gaps = 9/332 (2%)

Query: 1   MKLASYNNGRRDGQLMLVSRDLTQTVAVPAIAHTMQQLLDGWELLKPQLQELYDALNEGK 60
           MKLA+Y +G RDGQL++VSRDL        IA  +QQ+LD W  L PQLQ+LYD LN G+
Sbjct: 1   MKLATYKDGSRDGQLVVVSRDLGTAHYATGIASKLQQVLDDWGFLSPQLQDLYDQLNSGR 60

Query: 61  LPNTQTFDETKCLSPLPRAYQWADGSAYVNHVELVRKARGAEMPETFWTDPLFYQGGSDS 120
             +   FD  +C++PLPRAYQWADGSAY+NHVELVRKAR +E+PE+F+TDPL YQGGSD 
Sbjct: 61  ARHAFPFDPAQCMAPLPRAYQWADGSAYINHVELVRKARNSEVPESFYTDPLMYQGGSDD 120

Query: 121 FIAPKADIPLASEDWGIDFESEIAVITDDVPMGVSAENAAKHIKLLMLVNDVSLRNLIPA 180
           FI P  D+ + SE  GIDFE+EIAV+T DV MG +A+ A   I+L+M+ NDVSLRNLIPA
Sbjct: 121 FIGPCDDVVVPSEAMGIDFEAEIAVVTGDVKMGTNADQALDGIRLVMIANDVSLRNLIPA 180

Query: 181 ELAKGFGFFQSKPSSSFSPVAITPDELGHRWEDSKVHLPLITYLNGELFGRPNAGVDMTF 240
           ELAKGFGFFQSKP+++F PVA+T DELG  W+  +V+L + +  NG   G  +AG +MTF
Sbjct: 181 ELAKGFGFFQSKPATAFGPVAVTLDELGDAWDHGRVNLTVQSTWNGRKVGMCDAGPEMTF 240

Query: 241 NFSQLVSHVAKTRPLGAGAIIGSGTISN---------YDRSAGSSCLAEKRMLEVIADGK 291
           +F QL++HVAKTR L AG+IIGSGT+SN          +   G SC+AEKR +E I DGK
Sbjct: 241 HFGQLIAHVAKTRNLRAGSIIGSGTVSNKGITDANGRTEWPKGYSCIAEKRCIETIQDGK 300

Query: 292 ASTPFMRFGDTVRIEMLDDNGVSIFGSIDQKV 323
            ST FM+FGDT+RIE+   +G SIFG+IDQ +
Sbjct: 301 PSTDFMKFGDTIRIEVKGKDGASIFGAIDQAI 332


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: 332
Number of extensions: 10
Number of successful extensions: 2
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: 337
Length adjustment: 28
Effective length of query: 300
Effective length of database: 309
Effective search space:    92700
Effective search space used:    92700
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: 49 (23.5 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