GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Cupriavidus basilensis 4G11

Align fumarylacetoacetate (FAA) hydrolase (EC 3.7.1.2) (characterized)
to candidate RR42_RS16615 RR42_RS16615 hypothetical protein

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



>FitnessBrowser__Cup4G11:RR42_RS16615
          Length = 331

 Score =  247 bits (630), Expect = 3e-70
 Identities = 140/322 (43%), Positives = 181/322 (56%), Gaps = 2/322 (0%)

Query: 1   MKLATL-NQGRDGVLVVVSRDLAQAVKVPQIAATLQAALDDWNYCKPKLEAVYQRLNDGL 59
           MKL T+ N  RDG L +      QA+ V  I  T+Q A+D W+     L   Y+RL +G 
Sbjct: 1   MKLGTIDNWTRDGALALADTRSGQAIVVSHIVGTMQEAIDSWSKYSAPLHEEYRRLQEGT 60

Query: 60  EEGAFAFDQTACHSPLPRAYHWADGSAYVNHVELVRKARGAEMPESFWHDPLMYQGGADA 119
                   +    +PLPRAY   DG  Y  H+EL    R    PE     P  YQ  +D+
Sbjct: 61  LCATVPISELRWRAPLPRAYQLLDGGGYRPHLELGFSMRKQSFPEEMAEKPSFYQSVSDS 120

Query: 120 FIPPHSPIRLADEAWGIDLEGELAVITDDVPMGATPAEAASHIQLLMLVNDVSLRNLIPG 179
            + P     L  +  G D E EL V+T+DV   AT  E A+ I L+ L+ND+SLR     
Sbjct: 121 ILGPTEDFILGTDDLGTDFEAELVVVTNDVKQMATKVEGANGILLVGLMNDISLRLTQRV 180

Query: 180 ELAKGFGFYQSKPSSSFSPVAVTPDELGETWRDGKVHRPLVSHINGELFGQPDAGTDMTF 239
           E A+GFGFY  KP  + +P  VTPDELGE W + KV  P+    NGE+FG PD    M F
Sbjct: 181 EHARGFGFYHCKPKKTLAPFLVTPDELGEHWINFKVSLPVEVRWNGEVFGCPDGAEHMMF 240

Query: 240 NFPTLVAHAARTRPLGAGTIIGSGTVSNYDRSA-GSSCLAEKRMLEVVEHGEAKTPFLKF 298
           +F TLV+ A+R R L AGTIIG GTV+ YDR   G  C+ E+R L+++E GE +T +LK 
Sbjct: 241 DFATLVSEASRHRKLTAGTIIGGGTVATYDRDTFGQCCILERRALDILEFGEERTSWLKP 300

Query: 299 GDRVRIEMFDAAGQSIFGAIDQ 320
            DRVRIE+    G ++FGAIDQ
Sbjct: 301 DDRVRIEVRMPDGSTVFGAIDQ 322


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: 359
Number of extensions: 20
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: 327
Length of database: 331
Length adjustment: 28
Effective length of query: 299
Effective length of database: 303
Effective search space:    90597
Effective search space used:    90597
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: 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