GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Pseudomonas fluorescens FW300-N2C3

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate AO356_28710 AO356_28710 aldehyde dehydrogenase

Query= BRENDA::Q5P171
         (474 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28710 AO356_28710 aldehyde
           dehydrogenase
          Length = 473

 Score =  506 bits (1304), Expect = e-148
 Identities = 257/474 (54%), Positives = 319/474 (67%), Gaps = 6/474 (1%)

Query: 1   MQVFDMIINGKPVRA-GSTFDVVNPATGEVFARVQAGDASHVDQAVAAARAAFPGWSRTP 59
           M  + M+ING  V      FDV+NPATG VFAR  AG  + +D AV AA++AF  W  + 
Sbjct: 1   MHDYQMLINGARVDGENGHFDVINPATGTVFARCAAGSLAQLDLAVEAAQSAFIEWRYSS 60

Query: 60  DAERKRLMHALGAALEAHMPELMELVTKEAGKPLGGLNGVGSGMEVGGAIAWTHVTADLE 119
             +R++ + ++ A +E     L  L+  E GKPL       +  EV GA+AWT   A+ +
Sbjct: 61  HEDRRQRLQSIAADIEQDAESLARLIVLEQGKPLEL-----AFSEVMGAVAWTRYAAEQQ 115

Query: 120 LPVEVIQDNDDARIEVHRKPLGVVGSITPWNWPLMIAIWHVIPALRAGNTVVIKPSGMTP 179
           +PVE+++     RIE+HRKPLGVV SITPWNWP MIA+WH++PALRAGN V+ KPS +TP
Sbjct: 116 IPVELVEQTPSQRIELHRKPLGVVASITPWNWPFMIAVWHIMPALRAGNCVISKPSSLTP 175

Query: 180 TATIRFVELANAILPPGVLNIVTGESGVGSAIAKHPDINKIVFTGSTPTGKNIMQNAAGN 239
            +T+R VE+    +P GV+N VTGE G GSAI  H  I KIVFTGST TG+++M+ AAGN
Sbjct: 176 LSTLRLVEIIARHVPRGVINSVTGEQGFGSAITAHAGIQKIVFTGSTATGQSVMRGAAGN 235

Query: 240 LKRLTLELGGNDAGIVLPDVDPKAIAPKLFGVGFHNNGQTCACLKRLYVHDSIYEKVCAE 299
           LKRLTLELGGNDA IVLP    +A+A  +F   F N GQTCA LKRLY+H S YE     
Sbjct: 236 LKRLTLELGGNDAAIVLPGTPVEAVAEDIFQAAFLNMGQTCAALKRLYIHQSQYEAFAEA 295

Query: 300 LARIAKETVVGDGLVEGTELGPVQNKAQLDFVQELVEDARAHGARILSGGKARSGGGFFF 359
           L  IA+  VVGDGL  G   GPVQN  QL  V+ELV DARA GAR+L GG      GFF+
Sbjct: 296 LTVIARRQVVGDGLAPGVTFGPVQNLEQLTLVEELVADARAQGARVLCGGARLDRPGFFY 355

Query: 360 EPTVIADAKDGMRVVDEEQFGPVLPVIRYSDIEEVIARANNNENGLGGSIWSKDHAKAAE 419
            PT++AD  DG R+VDEEQFGPVLP+I Y D+E+V+ RAN  + GLGGS+W +D  +A  
Sbjct: 356 PPTLVADVTDGQRLVDEEQFGPVLPLIAYQDVEDVLRRANAGDMGLGGSVWGRDSEQAQA 415

Query: 420 LALRLECGTAWVNEHGAVQPDAPFGGVKQSGLGVEFGRYGLEEYTSIQTLKIMK 473
           LA RLECG AWVN H  +QP+ PFGG K SG GVEFG  GL E+T  Q L + K
Sbjct: 416 LASRLECGMAWVNCHAQIQPNTPFGGSKMSGFGVEFGLEGLLEFTGQQLLYVRK 469


Lambda     K      H
   0.317    0.136    0.405 

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: 689
Number of extensions: 27
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: 474
Length of database: 473
Length adjustment: 33
Effective length of query: 441
Effective length of database: 440
Effective search space:   194040
Effective search space used:   194040
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: 51 (24.3 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, the preprint on GapMind for carbon sources, 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