GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Sphingomonas koreensis DSMZ 15582

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Ga0059261_2160 Ga0059261_2160 acetyl-CoA acetyltransferases

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



>FitnessBrowser__Korea:Ga0059261_2160
          Length = 398

 Score =  428 bits (1100), Expect = e-124
 Identities = 225/399 (56%), Positives = 276/399 (69%), Gaps = 8/399 (2%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           M EA IVSTART IGKAYRGA N TE   L GH +  AV+RAG+DP  ++D+  G   Q 
Sbjct: 1   MREAAIVSTARTGIGKAYRGAFNTTEAPVLAGHVMNAAVERAGVDPARIDDIFWGVGNQW 60

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           G  GGN  R A+  AGLP +    T+DR+C SGL A+ALAARS++   ++IA+ GG ESI
Sbjct: 61  GTQGGNAGRMAVFAAGLPQSVPAFTLDRKCGSGLTALALAARSIIAGDIDIALSGGMESI 120

Query: 121 SLVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAA 180
           SL        +   + ++ A +   YM M++TAE VA+RYGISR RQDEY   SQ+R  A
Sbjct: 121 SLTVTKDAPRY--ANQSVLANEPHAYMPMIETAEIVAERYGISRARQDEYGAMSQQRAEA 178

Query: 181 AQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRG-- 238
               G F +EIAPI+ +  + DK       + +T++QDEG R  TTAE LAGLK V    
Sbjct: 179 GLASGAFAEEIAPITVEKAIFDKEGNRTGSERVTVTQDEGIRAGTTAEALAGLKTVWKDG 238

Query: 239 ----EGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGP 294
               EG  ITAGNASQLSDGA+A ++M    A A+G + LGI+RG  + GC PDEMGIGP
Sbjct: 239 QVVKEGRHITAGNASQLSDGAAAQIVMDRAIAEAEGKEILGIYRGFQAAGCAPDEMGIGP 298

Query: 295 VFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGM 354
           VFA+P+LL R GL V DIGLWELNEAFA Q LYCRD LGIDPEK NVNGGAI++GHP+GM
Sbjct: 299 VFAIPKLLGRAGLEVADIGLWELNEAFASQCLYCRDTLGIDPEKYNVNGGAIAIGHPFGM 358

Query: 355 SGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEI 393
           +GARL GHALIEGR+R  ++ VV+MC  GGMG+AGLFEI
Sbjct: 359 TGARLIGHALIEGRKRGVRWVVVSMCTAGGMGAAGLFEI 397


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: 515
Number of extensions: 21
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: 398
Length adjustment: 31
Effective length of query: 364
Effective length of database: 367
Effective search space:   133588
Effective search space used:   133588
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