GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Cupriavidus basilensis 4G11

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate RR42_RS31890 RR42_RS31890 acetyl-CoA acetyltransferase

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



>FitnessBrowser__Cup4G11:RR42_RS31890
          Length = 400

 Score =  456 bits (1172), Expect = e-133
 Identities = 232/400 (58%), Positives = 290/400 (72%), Gaps = 6/400 (1%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           M EAVIV+ ARTPIGKA+RGA N TE   L  H +   V+RAGIDP EV+DV++GAA QQ
Sbjct: 1   MREAVIVAVARTPIGKAFRGAFNDTEAPALGAHVVRAVVERAGIDPAEVDDVLIGAAAQQ 60

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           G  G N+ R   + AGLP +  G T+DR C+SGL  IA AA+S++    +I V GG ESI
Sbjct: 61  GTQGYNLGRLCAVAAGLPDSVPGMTMDRMCSSGLMTIATAAKSIICGEADIVVAGGAESI 120

Query: 121 SLVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAA 180
           SL QN   N + A   A+ A + D YMAM++TAE VA+RYGI+R  QDEY+L SQ+RTA 
Sbjct: 121 SLTQNKHKNAYRAQSEAVLARQPDAYMAMIETAEVVAQRYGIARAAQDEYALRSQQRTAE 180

Query: 181 AQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRG-- 238
           AQ+ G F+DEI P+ T+  + DKA     ++ + L+ DE  RP+T+A+ LA LK V    
Sbjct: 181 AQRQGLFDDEIVPLETRRALFDKAGALTGYETVRLALDECNRPDTSADSLAALKPVWSGG 240

Query: 239 ----EGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGP 294
               +G  ITAGNASQLSDGA+A ++MS + A  +GL+PLG +RGM   GC  DEMGIGP
Sbjct: 241 RTVPQGLHITAGNASQLSDGAAAVLLMSGEQAERRGLRPLGRYRGMAVAGCAADEMGIGP 300

Query: 295 VFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGM 354
           VFAVPRLL RHGL+V D+GLWELNEAFA QVLYCRD LGI   +LNVNGGAI++GHP+GM
Sbjct: 301 VFAVPRLLARHGLTVKDVGLWELNEAFACQVLYCRDTLGIPDARLNVNGGAIAIGHPFGM 360

Query: 355 SGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           SGAR+  HAL+E RRR A +AVVTMCVGGGMG+A LF+++
Sbjct: 361 SGARMTAHALLEARRRGAAHAVVTMCVGGGMGAAALFDVL 400


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: 481
Number of extensions: 21
Number of successful extensions: 2
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: 400
Length adjustment: 31
Effective length of query: 364
Effective length of database: 369
Effective search space:   134316
Effective search space used:   134316
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