GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HDOP-hydrol in Tatumella morbirosei LMG 23360

Align FAA hydrolase family protein (characterized, see rationale)
to candidate WP_038020839.1 HA49_RS04975 fumarylacetoacetate hydrolase family protein

Query= uniprot:A0A2E7P912
         (281 letters)



>NCBI__GCF_000757425.2:WP_038020839.1
          Length = 219

 Score =  129 bits (323), Expect = 7e-35
 Identities = 68/181 (37%), Positives = 104/181 (57%), Gaps = 3/181 (1%)

Query: 71  GKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKKTDWEVELGVV 130
           GK +C+G NYA H +E     P EPVVF K  +A+      + +  G  +   EVEL V+
Sbjct: 17  GKVVCVGSNYAKHISEMGSITPEEPVVFIKPETALCDLRQPLSLLSGLGEIHHEVELAVL 76

Query: 131 IGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQI---ERGGTWDKGKGCDTFGPIGPWLVT 187
           IG       E+  +  +AGY V  D++ R  Q    ++G  W+K KG D   P+  ++  
Sbjct: 77  IGSTLQQASEEQVLPAIAGYGVALDLTLRTVQAGLKKKGQPWEKSKGFDNSCPVSGFIPA 136

Query: 188 RDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTPPGV 247
            +   DPQ   + LE++G+  Q+GNTS M++ +  +++Y+SRF +L+PGD+I TGTP GV
Sbjct: 137 AEFNGDPQNTPLKLEINGEVRQSGNTSDMMYKIVPLIAYMSRFFTLRPGDIILTGTPEGV 196

Query: 248 G 248
           G
Sbjct: 197 G 197


Lambda     K      H
   0.316    0.138    0.419 

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: 181
Number of extensions: 11
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: 281
Length of database: 219
Length adjustment: 24
Effective length of query: 257
Effective length of database: 195
Effective search space:    50115
Effective search space used:    50115
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: 42 (22.0 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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