GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaG in Xanthobacter autotrophicus Py2

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_049776088.1 XAUT_RS04520 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase

Query= BRENDA::P77467
         (262 letters)



>NCBI__GCF_000017645.1:WP_049776088.1
          Length = 258

 Score =  300 bits (767), Expect = 3e-86
 Identities = 153/252 (60%), Positives = 187/252 (74%), Gaps = 3/252 (1%)

Query: 11  KGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAGQDLNDRN 70
           +G + LTLNRP+RLN+F +E+H  LA  L     DD  R +LLTGAGRGFCAGQDL DR 
Sbjct: 8   EGWVELTLNRPDRLNAFTEELHRSLAAAL-DAAADDACRAVLLTGAGRGFCAGQDLGDR- 65

Query: 71  VDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIVIAARSA 130
               GP  DLG ++E FYNPL+RR+  L KPV+CAVNGVAAGAGA +A   DIV+AARSA
Sbjct: 66  AKAEGPL-DLGATIEAFYNPLIRRIRALRKPVVCAVNGVAAGAGANIAFACDIVLAARSA 124

Query: 131 KFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQVVDDETL 190
           KF+ AF+K+GL+PD GGT+ LPR+ G ARA  L LL   +SAE+A  WG+IW+ VDD  L
Sbjct: 125 KFIQAFAKIGLVPDSGGTFFLPRLIGDARARALMLLAEPVSAEKAESWGLIWKAVDDAAL 184

Query: 191 ADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADYREGVSA 250
            D A+ LA HLA+QPT GL L KQA+N++  N LD QLDLERD QR AGR+ DYREGVSA
Sbjct: 185 MDEARALASHLASQPTQGLALTKQALNASAGNALDAQLDLERDLQREAGRTPDYREGVSA 244

Query: 251 FLAKRSPQFTGK 262
           F+ KR  +F+G+
Sbjct: 245 FMEKRPARFSGR 256


Lambda     K      H
   0.321    0.136    0.403 

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: 186
Number of extensions: 6
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: 262
Length of database: 258
Length adjustment: 24
Effective length of query: 238
Effective length of database: 234
Effective search space:    55692
Effective search space used:    55692
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 (21.8 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