GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Moritella dasanensis ArB 0140

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_017223337.1 A923_RS0119275 acetyl-CoA C-acetyltransferase

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



>NCBI__GCF_000276805.1:WP_017223337.1
          Length = 403

 Score =  210 bits (535), Expect = 5e-59
 Identities = 138/409 (33%), Positives = 216/409 (52%), Gaps = 35/409 (8%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           M +  IV+  RT +G ++ G+L   + ATL   AI+ A+  A ++P+ V++V++G  +  
Sbjct: 1   MNKVFIVAAKRTALG-SFGGSLAGVDAATLGATAIKGALAAAKVNPEHVDEVIVGNVISA 59

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           G  G    R+A ++AG+P +    T++  C SG++ I   A  +     +I V  G ES+
Sbjct: 60  GQ-GMGPGRQAAMQAGIPASVPAYTLNMICGSGMKTIMDGAAHIKAGDADIVVAAGMESM 118

Query: 121 SLVQ---------NDKMNTFHAVDPALEAIKGDVY----MAMLDTAETVAKRYGISRERQ 167
           S +            KM     VD  +     DV+    M M  TAE +  ++G++RE+Q
Sbjct: 119 SNIPYLMPAKTRFGSKMGNMTMVDAMINDGLTDVFNNYHMGM--TAENIVDQFGLTREQQ 176

Query: 168 DEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTA 227
           D +++ SQ +  AA    +F DEI P+  K          V  +  + + DE P+  T+ 
Sbjct: 177 DTFAVGSQHKAVAAIAAERFVDEIVPVEIK----------VRRQTQSFATDEYPKDNTSV 226

Query: 228 EGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEP 287
           EGLA L+       ++TA NAS ++DGASA ++ S       GL+P+         G +P
Sbjct: 227 EGLAKLRPAFKTDGSVTAANASGINDGASAIILASAAAVEKYGLEPMAELIAYGQGGVDP 286

Query: 288 DEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKL----GID----PEKL 339
             MG+GPV A+ + LKR  +S++ + L ELNEAFA Q L     L     +D     +K 
Sbjct: 287 QVMGLGPVPAIEQALKRADMSLEQMELLELNEAFAAQALGVMTNLTQEHNVDMDWFADKT 346

Query: 340 NVNGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388
           NVNGGAI++GHP G SG R+    L E ++R   Y + ++C+GGGMG+A
Sbjct: 347 NVNGGAIALGHPLGASGGRITVTLLHEMQKRGVDYGLASLCIGGGMGTA 395


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: 427
Number of extensions: 32
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: 403
Length adjustment: 31
Effective length of query: 364
Effective length of database: 372
Effective search space:   135408
Effective search space used:   135408
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