GapMind for catabolism of small carbon sources

 

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

Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate Pf1N1B4_3234 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)

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



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3234 Beta-ketoadipyl CoA
           thiolase (EC 2.3.1.-)
          Length = 400

 Score =  323 bits (827), Expect = 7e-93
 Identities = 189/401 (47%), Positives = 253/401 (63%), Gaps = 11/401 (2%)

Query: 1   MQEVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQT-GLSGEQVDEVILGQVLTA 59
           M++V I  A RT IG F G L+A+ A +L A  I+ L+ +   +    VDEV LG    A
Sbjct: 1   MRDVYICDAIRTPIGRFGGGLSAVRADDLAAVPIKALMARNPSVDWSAVDEVFLGCANQA 60

Query: 60  GS-GQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENM 118
           G   +N AR A +LAGLP  +P +TLN++C SG+ A+    +AI  G+ E+ IAGG+E+M
Sbjct: 61  GEDNRNVARMALLLAGLPETIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120

Query: 119 SLAPYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGI-----TAENLVDKYGISRE 173
           S AP+V+  A       + K+ D+ I     +       G+     TA+N+ D Y ISR 
Sbjct: 121 SRAPFVMGKADAAFSR-NMKLEDTTIGWRFINPLMKAQYGVDAMPQTADNVADDYRISRA 179

Query: 174 EQDAFAAASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLK 233
           +QDAFA  SQQ+  AA   G FA+EI  + I  +KG+ V    DE PRA TT E+L KLK
Sbjct: 180 DQDAFALRSQQRTAAAQAAGFFAEEIVEVRIAHKKGESVV-TQDEHPRADTTLETLAKLK 238

Query: 234 PAFKKDGSVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGP 293
           P    D +VTAGNAS +NDGAAA+IL SAE  K  GL   AK+   ++AGV P +MGIGP
Sbjct: 239 PVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTARAKVLGMSSAGVAPRVMGIGP 298

Query: 294 VSATRRCLDKAGWSLEQLDLIEANEAFAAQSLAVARELKW--DMDKVNVNGGAIALGHPI 351
           V A R+  ++ G ++   D+IE NEAFA+Q LAV REL    D  +VN NGGAIALGHP+
Sbjct: 299 VPAVRKLTERLGLAVSDFDVIELNEAFASQGLAVLRELGLADDSAQVNPNGGAIALGHPL 358

Query: 352 GASGCRVLVSLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           G SG R++++ LH++ K   KKGLAT+C+G GQG+ALA+ER
Sbjct: 359 GMSGARLVLTALHQLEKTGGKKGLATMCVGVGQGLALAIER 399


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: 395
Number of extensions: 18
Number of successful extensions: 4
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: 400
Length adjustment: 31
Effective length of query: 362
Effective length of database: 369
Effective search space:   133578
Effective search space used:   133578
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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