GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Pseudomonas fluorescens FW300-N1B4

Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate Pf1N1B4_5835 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= reanno::pseudo5_N2C3_1:AO356_21640
         (393 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5835
          Length = 393

 Score =  677 bits (1748), Expect = 0.0
 Identities = 343/393 (87%), Positives = 374/393 (95%)

Query: 1   MQEVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTAG 60
           MQEVVIVAATRTAIGSFQGSLA + A +LGAAVIR+LL QTGL   QVDEVI+GQVLTAG
Sbjct: 1   MQEVVIVAATRTAIGSFQGSLANVSAVDLGAAVIRQLLAQTGLDPAQVDEVIMGQVLTAG 60

Query: 61  SGQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
           +GQNPARQA+I AGLP AVPA+TLNKVCGSGLKALHL AQAIRCGDAEVIIAGG ENMSL
Sbjct: 61  AGQNPARQAAIKAGLPFAVPAMTLNKVCGSGLKALHLAAQAIRCGDAEVIIAGGQENMSL 120

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREEQDAFAA 180
           + YV+P ARTGLRMGHA+++D+MI+DGLWDAFNDYHMGITAENL +KY ++RE+QDAFAA
Sbjct: 121 SNYVMPGARTGLRMGHAQIVDTMISDGLWDAFNDYHMGITAENLAEKYSLTREQQDAFAA 180

Query: 181 ASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKPAFKKDG 240
           ASQQKAVAAIE GRFADEITPILIPQRKGDP++FATDEQPRAGTTA+SLGKLK AFKKDG
Sbjct: 181 ASQQKAVAAIEAGRFADEITPILIPQRKGDPLSFATDEQPRAGTTADSLGKLKAAFKKDG 240

Query: 241 SVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVSATRRC 300
           SVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKI+AYANAGVDPAIMGIGPVSATRRC
Sbjct: 241 SVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKIAAYANAGVDPAIMGIGPVSATRRC 300

Query: 301 LDKAGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIALGHPIGASGCRVLV 360
           LDK GWS+ QLDLIEANEAFAAQSLAVA++L+WD++KVNVNGGAIALGHPIGASGCRVLV
Sbjct: 301 LDKTGWSIGQLDLIEANEAFAAQSLAVAKDLEWDLNKVNVNGGAIALGHPIGASGCRVLV 360

Query: 361 SLLHEMIKRDAKKGLATLCIGGGQGVALALERA 393
           +LLHEMIK+DAKKGLATLCIGGGQGVALA+ERA
Sbjct: 361 TLLHEMIKQDAKKGLATLCIGGGQGVALAIERA 393


Lambda     K      H
   0.317    0.133    0.376 

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: 603
Number of extensions: 16
Number of successful extensions: 1
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: 393
Length of database: 393
Length adjustment: 31
Effective length of query: 362
Effective length of database: 362
Effective search space:   131044
Effective search space used:   131044
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