Aligments for a candidate for fadA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for fadA in Dinoroseobacter shibae DFL-12

Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate 3606642 Dshi_0074 acetyl-CoA acetyltransferase (RefSeq)

Query= reanno::acidovorax_3H11:Ac3H11_2994
         (397 letters)



>lcl|FitnessBrowser__Dino:3606642 Dshi_0074 acetyl-CoA
           acetyltransferase (RefSeq)
          Length = 392

 Score =  468 bits (1204), Expect = e-136
 Identities = 238/387 (61%), Positives = 287/387 (74%)

Query: 9   IVIVGAARTPMGSLQGDFSSLAAHDLGGAAIKAAIERAGVSPDAVGEVLFGNCLMAGQGQ 68
           + I GAARTPMG  QG FS ++A  LGGAAI  A+  AGV+P  V E+L G  L AGQGQ
Sbjct: 4   VAICGAARTPMGGFQGVFSDVSAAQLGGAAIAGALADAGVAPAQVNELLMGCVLPAGQGQ 63

Query: 69  APARQAAFKGGLPKGAGAVTLSKMCGSGMKAAMMAHDMLLAGSHDVMVAGGMESMTNAPY 128
           APARQA +  GL     A TL+KMCGSGMKAAM+A D +  G  D++VAGGMESMTNAPY
Sbjct: 64  APARQAGYAAGLGDAVPATTLNKMCGSGMKAAMIACDQIALGQSDLVVAGGMESMTNAPY 123

Query: 129 LLQKGRGGYRLGHDRIFDHMMLDGLEDAYEAGRSMGTFGEDCAAKYSFTREQQDAFATAS 188
           LL K RGG R+GH ++ DHM LDGLEDAY+ GR MGTF EDCA  + FTR  QD +A  S
Sbjct: 124 LLDKMRGGARIGHGQVIDHMFLDGLEDAYDKGRLMGTFAEDCAEAFQFTRAAQDTYALGS 183

Query: 189 VQRAKAATESGAFAAEIVPVTVKTRAGETVVSVDEGPGKVKLEKIATLKPAFKKDGTITA 248
           ++ A AA  S AFA E+VPVTV  R GETVV  DE P   + EKI  LKPAF+KDGT+TA
Sbjct: 184 LENALAAEASEAFAMELVPVTVSGRKGETVVIRDEQPAAARPEKIPHLKPAFRKDGTVTA 243

Query: 249 ASSSSINDGAAALVMMRESTAKKLGAKPLARIVSHATHAQEPEWFATAPLGATQKALAKA 308
           A+SSSI+DGAAALV+     A+  G    AR++ HA+HAQ+P  F TAP+ A +K L + 
Sbjct: 244 ANSSSISDGAAALVLADAGQAEAHGLPVRARVLGHASHAQKPALFPTAPVPAARKLLDRL 303

Query: 309 GWQVGDVQLWEINEAFAVVPMALMKELDLPHDKVNVNGGACALGHPIGASGARIMVTLIH 368
           GW V DV LWE+NEAFAVVPMA M E+ +P +K+NVNGGACALGHPIGASGARI+VTL++
Sbjct: 304 GWCVADVDLWEVNEAFAVVPMAFMHEMGVPREKMNVNGGACALGHPIGASGARILVTLLN 363

Query: 369 ALKARGLTKGLATLCIGGGEATAVALE 395
           A++AR L +G+A +CIGGGE TA+ALE
Sbjct: 364 AMEARDLKRGVAAICIGGGEGTAIALE 390


Lambda     K      H
   0.317    0.131    0.376 

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: 511
Number of extensions: 19
Number of successful extensions: 1
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: 397
Length of database: 392
Length adjustment: 31
Effective length of query: 366
Effective length of database: 361
Effective search space:   132126
Effective search space used:   132126
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources