GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HDOP-hydrol in Thiothrix lacustris DSM 21227

Align FAA hydrolase family protein (characterized, see rationale)
to candidate WP_028488570.1 Q394_RS0106530 fumarylacetoacetate hydrolase family protein

Query= uniprot:A0A2E7P912
         (281 letters)



>NCBI__GCF_000621325.1:WP_028488570.1
          Length = 294

 Score =  159 bits (401), Expect = 9e-44
 Identities = 88/206 (42%), Positives = 123/206 (59%), Gaps = 9/206 (4%)

Query: 74  ICIGLNYADHAAESNLPI------PAEPVVFNKWTSAVVGPNDDVKI-PRGSKKTDWEVE 126
           +C+GLNY +HA E+   I      P  P+VF K  ++V+G +  V   P    + DWE E
Sbjct: 81  MCLGLNYLEHAEETANQIGRTGKAPQYPIVFTKCPTSVIGQDAVVPFDPDTCSQLDWEAE 140

Query: 127 LGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGPIGPWLV 186
           LGVV+GKGG  I   +A+ HV GY V+ND+S R+ Q+     +  GK  D   P+GPW+V
Sbjct: 141 LGVVLGKGGKKIAAANALDHVFGYTVINDLSARDIQLSHK-QYFLGKSLDGGCPMGPWIV 199

Query: 187 TRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTPPG 246
           T D++ADPQ L +   V+G   Q  NT  MIF VA I+ +LSR M+L+ GDVI+TGTP G
Sbjct: 200 TADDIADPQNLAIACRVNGVTKQASNTRNMIFNVASIIEWLSRGMTLEAGDVIATGTPSG 259

Query: 247 VGMGVKPEAVYLRAGQTMRLGIDGLG 272
           VG  V+    +L  G  +   ++ +G
Sbjct: 260 VGF-VREPPEFLLPGDVVECEVESVG 284


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: 245
Number of extensions: 16
Number of successful extensions: 3
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: 294
Length adjustment: 26
Effective length of query: 255
Effective length of database: 268
Effective search space:    68340
Effective search space used:    68340
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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