GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Algiphilus aromaticivorans DG1253

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_043764857.1 U743_RS01125 glutamate-1-semialdehyde 2,1-aminomutase

Query= SwissProt::Q5JEW1
         (445 letters)



>NCBI__GCF_000733765.1:WP_043764857.1
          Length = 426

 Score =  122 bits (307), Expect = 2e-32
 Identities = 93/308 (30%), Positives = 141/308 (45%), Gaps = 27/308 (8%)

Query: 37  PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96
           P  IE  EG  + DVDGN + D+    G + +GH HP VV+A++ QA +   +       
Sbjct: 33  PRFIETAEGAWMTDVDGNRYIDYIGSWGPMLLGHGHPDVVQAVQAQAGRGISFGAPT--- 89

Query: 97  ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156
           E  + +AE + E  P     K+   +SG EA  +A++L +  +GR   L F   +HG + 
Sbjct: 90  EAEVEMAELIRERVPS--MEKLRLNSSGTEATMSAVRLARAASGRDGVLKFEGCYHGHSD 147

Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216
           ++L    S  +      P+ PG+               D  +     T   LD + E   
Sbjct: 148 SLLVKAGSGALTFGE--PSSPGIP-------------ADIAKHTRTATYNDLDSVREAFA 192

Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276
           ++  P  IG +  EP+ G    V P  GF + L+   DE G LL  DEV  G  R     
Sbjct: 193 QN--PGAIGCVIVEPVAGNMNMVPPAPGFLEGLRSICDEQGALLIFDEVMTGF-RVHPGG 249

Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI----TFDKPGRHATTFGGNPVAIAAGI 332
           A   +GV PDL   GK +GGG+P+     RA +    + + P   A T  G+P+A AAG+
Sbjct: 250 AQALYGVTPDLTALGKIVGGGMPVGAFGGRAAVMDMLSPEGPVYQAGTLSGSPLATAAGL 309

Query: 333 EVVEIVKE 340
             +  + +
Sbjct: 310 ATLRAIDD 317


Lambda     K      H
   0.320    0.141    0.418 

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: 421
Number of extensions: 24
Number of successful extensions: 5
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: 445
Length of database: 426
Length adjustment: 32
Effective length of query: 413
Effective length of database: 394
Effective search space:   162722
Effective search space used:   162722
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: 51 (24.3 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