GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Marinobacter guineae M3B

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_099619682.1 CLH62_RS18535 acetyl-CoA C-acyltransferase FadA

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



>NCBI__GCF_002744735.1:WP_099619682.1
          Length = 391

 Score =  246 bits (629), Expect = 6e-70
 Identities = 160/395 (40%), Positives = 216/395 (54%), Gaps = 17/395 (4%)

Query: 3   EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQQG 61
           + V+V   RTP+G+A  G        TL    IE   +R   +DPKEVEDV+ G   Q  
Sbjct: 7   DVVVVDCVRTPMGRAKNGCFRNVRAETLSAALIEALFERNPKLDPKEVEDVIWGCVNQTK 66

Query: 62  ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121
             G N+AR+  L   +P  +A  T++R C S + AI  AA++++    ++ V GG E + 
Sbjct: 67  EQGFNVARQISLLTRIPHESAAQTVNRLCGSSMSAIHTAAQAIMTGNGDVFVVGGVEHMG 126

Query: 122 LVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAAA 181
            V    M      +PA           M  TAE +AK +GI+R++QDE+   S R    A
Sbjct: 127 HVP---MTEGFDHNPAASKYTAKASNMMGLTAEMLAKMHGITRKQQDEFGARSHRLAHEA 183

Query: 182 QQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLK-AVRGEG 240
              G+FN+EI PI           G V      + +DE  RP+TT E L  LK A   + 
Sbjct: 184 TLEGRFNNEIVPIEGH-----DENGFVKL----IEEDETIRPDTTVESLGQLKPAFDPKN 234

Query: 241 FTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVPR 300
            T+TAG +SQL+DGA+A V+MS + A A GLKP+   R M   GC+P  MG GPV A  +
Sbjct: 235 GTVTAGTSSQLTDGAAAMVLMSAERAEALGLKPIARVRSMAVAGCDPAIMGYGPVPATKK 294

Query: 301 LLKRHGLSVDDIGLWELNEAFAVQ---VLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGA 357
            LKR GL V+DI  WELNEAFA Q   VL     LG+  EK+N+NGGAI++GHP G SGA
Sbjct: 295 ALKRAGLKVEDIDFWELNEAFAGQSLPVLKDLKLLGVMAEKVNLNGGAIALGHPLGCSGA 354

Query: 358 RLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392
           R++   L   + +  K  V TMC+G G G A ++E
Sbjct: 355 RISTTLLNVMQAKGGKLGVSTMCIGLGQGIATVWE 389


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: 397
Number of extensions: 17
Number of successful extensions: 6
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: 395
Length of database: 391
Length adjustment: 31
Effective length of query: 364
Effective length of database: 360
Effective search space:   131040
Effective search space used:   131040
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 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