GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3606642
          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.

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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