GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Pseudomonas fluorescens GW456-L13

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate PfGW456L13_2538 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= BRENDA::Q0K368
         (391 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2538
          Length = 382

 Score =  377 bits (968), Expect = e-109
 Identities = 205/393 (52%), Positives = 268/393 (68%), Gaps = 13/393 (3%)

Query: 1   MAEAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVG 60
           M EAYIV A+RT  GR+ G LS  H ADL A VL ALVER        +DVI GCV  +G
Sbjct: 1   MPEAYIVDALRTPTGRRKGGLSQIHAADLGAHVLRALVERNAIPDEDYDDVIFGCVDTIG 60

Query: 61  EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120
             AG++AR + LA+ L +SVPGT++DRQCGSSQQA+HFAAQAVMSG  D+VIA GV++MT
Sbjct: 61  PLAGDIARTSWLAAGLSQSVPGTTIDRQCGSSQQAVHFAAQAVMSGTQDVVIAGGVQTMT 120

Query: 121 RVPMGLSSQLPAKNGFGVP--KSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYAL 178
           ++P+  +       GF  P   S G   RY     +QF  A+MIA K+DLSR QL+AY+L
Sbjct: 121 QIPISSAMIAAEPLGFTDPFSGSEGWVRRYGAQPPTQFRSAQMIAEKWDLSRAQLEAYSL 180

Query: 179 QSHQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVKLIAEGG 238
           +SH+RA+ A + GRF  EI+P+         G +H  DE  R   +LE +  ++ +    
Sbjct: 181 ESHRRALQAIEQGRFNREIVPLA--------GVLH--DETPR-QTSLEKMAELEFLFGCD 229

Query: 239 RVTAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVA 298
           RVTAA +SQ CD A+ +++V+EA LK+ G+ P AR+H ++V   DP+ ML AP+PAT  A
Sbjct: 230 RVTAAVSSQTCDAASAMLIVSEAALKRYGLTPRARIHHLSVRAEDPIWMLTAPIPATAYA 289

Query: 299 LKKAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLMT 358
           LK+AG+++ DID  E+NEAFA V +AWLK TG    + NV+GGAIALGHPLG +G +LM 
Sbjct: 290 LKRAGMKLEDIDRVEINEAFASVAMAWLKETGYPHEQTNVNGGAIALGHPLGATGTRLMC 349

Query: 359 TLVHALHTHGKRYGLQTMCEGGGLANVTIVERL 391
           TL+H L   G R+G+QTMCEGGG ANVTI+ERL
Sbjct: 350 TLLHELERSGGRFGMQTMCEGGGQANVTIIERL 382


Lambda     K      H
   0.317    0.132    0.379 

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: 454
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: 391
Length of database: 382
Length adjustment: 30
Effective length of query: 361
Effective length of database: 352
Effective search space:   127072
Effective search space used:   127072
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 (21.7 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