GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Rhodobacter maris JA276

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_097068496.1 CRO22_RS02395 acetyl-CoA C-acetyltransferase

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



>NCBI__GCF_900217815.1:WP_097068496.1
          Length = 391

 Score =  251 bits (640), Expect = 3e-71
 Identities = 155/401 (38%), Positives = 218/401 (54%), Gaps = 21/401 (5%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           MT  VIVS ART +G ++ GA   T    L    IE  V RAGID  EV + ++G  +  
Sbjct: 1   MTNVVIVSAARTAVG-SFNGAFANTPAHDLGAAVIEAVVARAGIDKAEVSETILGQVLSA 59

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           G  G N AR+A ++AGLP+ +A   I++ C SGL+ +AL A+ +     +I V GG ES+
Sbjct: 60  GQ-GQNPARQAHIKAGLPIESAAWGINQVCGSGLRTVALGAQHIQLGDADIVVAGGQESM 118

Query: 121 SLVQN-------DKMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEYS 171
           SL  +        KM     +D  ++    D +    M  TAE VA ++ ISRE QD  +
Sbjct: 119 SLSPHVAHLRAGTKMGDMKMIDSMIKDGLWDAFNGYHMGQTAENVAAQWQISREMQDALA 178

Query: 172 LESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLA 231
           L SQ +  AAQ+ GKF DEI P + K              DI +  DE  R   T E + 
Sbjct: 179 LASQNKAEAAQKAGKFTDEIVPFTVK----------TRKGDIVVDADEYIRHGATLESMQ 228

Query: 232 GLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMG 291
            LK    +  T+TAGNAS ++DGA+  ++M+++ AA +GL P+       + G +P  MG
Sbjct: 229 KLKPAFIKDGTVTAGNASGINDGAAVVLLMTEEEAAKRGLTPMARIASWATAGLDPSIMG 288

Query: 292 IGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHP 351
            GP+ A  + L++ G +  D+ L E NEAFA Q       +G D  K+NVNGGAI++GHP
Sbjct: 289 CGPIPASRKALEKAGWTAADLDLIEANEAFAAQACAVNKDMGWDTAKVNVNGGAIAIGHP 348

Query: 352 YGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392
            G SG R+    + E +R  AK  + T+C+GGGMG A   E
Sbjct: 349 IGASGCRILNTLVFEMKRSGAKKGLATLCIGGGMGVAMCLE 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: 387
Number of extensions: 17
Number of successful extensions: 4
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