GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Burkholderia phytofirmans PsJN

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate BPHYT_RS09565 BPHYT_RS09565 acetyl-CoA acetyltransferase

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



>FitnessBrowser__BFirm:BPHYT_RS09565
          Length = 392

 Score =  469 bits (1207), Expect = e-137
 Identities = 244/394 (61%), Positives = 297/394 (75%), Gaps = 2/394 (0%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           MT+AVIVSTART + K++RG  N T GATL GH  + AV+RA +DP  VEDV+MG A  +
Sbjct: 1   MTDAVIVSTARTGLAKSWRGGFNMTHGATLGGHVTQAAVERAKLDPARVEDVIMGCANPE 60

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           GATG NIAR+  LRAGLPV+  G T++R C+SGLQ IALAA+ V+    ++ V GG ESI
Sbjct: 61  GATGMNIARQIALRAGLPVSVPGMTVNRFCSSGLQTIALAAQRVIAGEGDVFVAGGVESI 120

Query: 121 SLVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAA 180
           S VQN+ MN     +  L   K ++Y +ML TAE VAKRY IS+ERQDEY   SQ+R AA
Sbjct: 121 SCVQNE-MNHHMLTEGWLSQNKPEIYWSMLQTAENVAKRYSISKERQDEYGARSQQRAAA 179

Query: 181 AQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGEG 240
           A + GKF DEI P++   GV DKA+G +  K++T+S DEG R +TT EG++ ++     G
Sbjct: 180 ALEAGKFKDEIVPLTVLAGVADKASGRLFTKEVTVSGDEGIRADTTLEGVSKIRTALPGG 239

Query: 241 FTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVPR 300
             ITAGNASQ SDGASA V+M+ K A  +GL+PLGIFRG    GCEPDEMGIGPVFAVP+
Sbjct: 240 -VITAGNASQFSDGASACVVMNAKVAEREGLQPLGIFRGFAVAGCEPDEMGIGPVFAVPK 298

Query: 301 LLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARLA 360
           LLK+ GL V+DI LWELNEAFAVQVLYC DKLGI  ++LNVNGGAI+VGHPYG+SGARL 
Sbjct: 299 LLKQAGLKVEDIDLWELNEAFAVQVLYCADKLGIPQDRLNVNGGAIAVGHPYGVSGARLT 358

Query: 361 GHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           GHALIEG+RR AK  VVTMC+GGG G+AGLFE+V
Sbjct: 359 GHALIEGKRRGAKLVVVTMCIGGGQGAAGLFEVV 392


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: 511
Number of extensions: 17
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: 392
Length adjustment: 31
Effective length of query: 364
Effective length of database: 361
Effective search space:   131404
Effective search space used:   131404
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