GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Halioglobus japonicus S1-36

Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_084201012.1 C0029_RS15270 glutamate-1-semialdehyde 2,1-aminomutase

Query= BRENDA::Q9FNK4
         (475 letters)



>NCBI__GCF_002869505.1:WP_084201012.1
          Length = 426

 Score =  134 bits (336), Expect = 8e-36
 Identities = 94/302 (31%), Positives = 151/302 (50%), Gaps = 23/302 (7%)

Query: 59  PVVFSRANGSTIWDPEGKRYIDFLAAYSAVNQGHCHPKIMKALQEQVEKLTLSSRAFYND 118
           PV   R++G+ ++D EGK YID++ ++  +  GH HP + +A+ +Q EK  LS  A    
Sbjct: 33  PVFIDRSDGARVYDCEGKAYIDYVLSWGPMIMGHNHPAVREAVIKQSEK-GLSFGAPTEL 91

Query: 119 KFPVFAERLTNMFGYDMVLPMNTGAEGVETALKLARKWGHEKKNIPKDEAIIVSCCGCFH 178
           +  +       M G D+V  +N+G E   +A++LAR  G+  ++       IV   GC+H
Sbjct: 92  EIQLADRICEIMPGMDLVRMVNSGTEATMSAIRLAR--GYTGRDT------IVKFEGCYH 143

Query: 179 GRTLAIVSMSCDNDATRGFGPLLPG--------NLKVDFGDADSLEKIFKEKGDRIAGFL 230
           G + +++  +     T G  P  PG         + + + D + +   F E GD IA  +
Sbjct: 144 GHSDSLLVKAGSGALTMGV-PSSPGVPAALADHTMTLTYNDPEGVRAAFAEHGDSIACVI 202

Query: 231 FEPIQGEAGVIIPPDGYLKAVRELCTKYNVLMIADEVQSGLARSGKMLACDWEEIRPDMV 290
            EP+ G    I P  G+L+ +RE C     ++I DEV +G  R G   A  +  +  D+ 
Sbjct: 203 VEPVAGNMNCIPPEPGFLETLRECCDVSGAVLILDEVMTGF-RFGLQGAQGFFGVEADLT 261

Query: 291 ILGKALGGGVIPVSAVLADKDVMLHIK---PGQHGSTFGGNPLASAVAMASLDVIVEEKL 347
            LGK +GGG +PV A    +++M  I    P     T  GNP+A A  +A+LD+I  +  
Sbjct: 262 TLGKVVGGG-MPVGAFGGKREIMEQIAPLGPVYQAGTLSGNPIAMAAGLATLDIISADGF 320

Query: 348 VE 349
            E
Sbjct: 321 YE 322


Lambda     K      H
   0.318    0.136    0.400 

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: 482
Number of extensions: 17
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: 475
Length of database: 426
Length adjustment: 33
Effective length of query: 442
Effective length of database: 393
Effective search space:   173706
Effective search space used:   173706
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: 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