GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Flavobacterium sp. LM5

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_078211525.1 BXU11_RS06925 acetyl-CoA C-acyltransferase

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



>NCBI__GCF_002017945.1:WP_078211525.1
          Length = 393

 Score =  263 bits (673), Expect = 5e-75
 Identities = 152/397 (38%), Positives = 225/397 (56%), Gaps = 7/397 (1%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRA-GIDPKEVEDVVMGAAMQ 59
           M  A IV   RT +GKA +G         L    I++ +      D   ++DV++G AM 
Sbjct: 1   MKTAYIVKAYRTAVGKAPKGVFRFKRPDELAAETIQYMMNELPDFDKTRIDDVMVGNAMP 60

Query: 60  QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119
           +   G N+ R   L         G T++R CASGL+ I +A   +        + GG ES
Sbjct: 61  EAEQGLNVGRLISLMGLKVDDVPGVTVNRYCASGLETIGMATAKIQSGMAHCIIAGGAES 120

Query: 120 ISLVQNDKMNTFHAVDPALEAIKG--DVYMAMLDTAETVAKRYGISRERQDEYSLESQRR 177
           +S +    M  +        A  G  D Y  M  T+E VAK++ ISR  QDE++ +S  +
Sbjct: 121 MSYIP---MGGYKPTPDYKVAAAGHEDYYWGMGLTSEAVAKQFNISRADQDEFAFQSHNK 177

Query: 178 TAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVR 237
              AQ  GKF+++I PI+ +   +++  G    K   +++DEGPR  T+ E LAGL+ V 
Sbjct: 178 ALKAQAEGKFDNQIVPITVEQTFINE-NGKKETKSYVVTKDEGPRAGTSLEALAGLRPVF 236

Query: 238 GEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFA 297
               ++TAGN+SQ+SDGA+  ++MS++      ++P+       S G EP  MGIGPV A
Sbjct: 237 AADGSVTAGNSSQMSDGAAFVLVMSEEMVKELNIQPIARLVNFASAGVEPRIMGIGPVKA 296

Query: 298 VPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGA 357
           +P+ LK+ GL+++DI L ELNEAFA Q L    +L ++P+ +NVNGGAI++GHP G +GA
Sbjct: 297 IPKALKQAGLTLNDIDLIELNEAFASQALAVTRELNLNPDIINVNGGAIALGHPLGCTGA 356

Query: 358 RLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           +L+     E +RR  KY +V+MCVG G GSAG+FE+V
Sbjct: 357 KLSVQLFDEMKRRGNKYGIVSMCVGTGQGSAGIFELV 393


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: 433
Number of extensions: 20
Number of successful extensions: 3
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: 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 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