GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Dechlorosoma suillum PS

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Dsui_0976 Dsui_0976 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-20679
         (395 letters)



>FitnessBrowser__PS:Dsui_0976
          Length = 393

 Score =  219 bits (559), Expect = 8e-62
 Identities = 145/391 (37%), Positives = 212/391 (54%), Gaps = 24/391 (6%)

Query: 5   VIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGATG 64
           VIVS ARTP+G  ++G  N+     L   AI+ AV+RAGI P++VE+VV G  +Q G  G
Sbjct: 6   VIVSVARTPMG-GFQGDFNSLTAPQLGATAIKAAVERAGIKPEQVEEVVFGNVLQAGV-G 63

Query: 65  GNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISLVQ 124
              AR+A L AGLP++   TTI + C S L+++ +   S+L    EI V GG ES+S   
Sbjct: 64  QAPARQAALGAGLPLSAGCTTIHKVCGSALKSVMMVHDSLLAGSYEIGVAGGQESMSNAP 123

Query: 125 --------NDKMNTFHAVDPALEAIKGDVYMA---MLDTAETVAKRYGISRERQDEYSLE 173
                     ++     +D        D Y     M   AE  A+ YG +RE QDE++++
Sbjct: 124 YLLPKARGGYRLGHGQLLDHMFFDGLEDAYQKGRLMGTFAEECAESYGFTREAQDEWAIQ 183

Query: 174 SQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGL 233
           S  R   A + G F  EIAP+          T A    D+ + QDE P  +   E +  L
Sbjct: 184 STVRAQKAIKEGLFKWEIAPV----------TIAGKKGDVVVDQDEQPL-KAQIEKIPAL 232

Query: 234 KAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIG 293
           K    +  T+TA N+S +SDGA+A V+M +  A   GL P+    G  ++  EP+     
Sbjct: 233 KPAFKKDGTVTAANSSSISDGAAALVLMKESKAKVLGLAPIAKIVGHTTHAQEPNLFTTA 292

Query: 294 PVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYG 353
           PVFA+ +L+++ G +V D+ LWE+NEAFAV  +     L +DP K+NV+GGA ++GHP G
Sbjct: 293 PVFAMEKLMQKTGWNVADVDLWEINEAFAVVTMAAIKDLKLDPAKVNVHGGACALGHPIG 352

Query: 354 MSGARLAGHALIEGRRRKAKYAVVTMCVGGG 384
            SGAR+    +   ++   K  V ++C+GGG
Sbjct: 353 ASGARILVTLIGALKQYGKKKGVASLCIGGG 383


Lambda     K      H
   0.316    0.134    0.378 

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: 414
Number of extensions: 21
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 395
Length of database: 393
Length adjustment: 31
Effective length of query: 364
Effective length of database: 362
Effective search space:   131768
Effective search space used:   131768
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 (21.6 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