GapMind for catabolism of small carbon sources

 

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

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Pf1N1B4_171 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_171
          Length = 477

 Score =  349 bits (895), Expect = e-100
 Identities = 191/478 (39%), Positives = 282/478 (58%), Gaps = 11/478 (2%)

Query: 5   LLINGELV-SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQTTPK 61
           +LI G+ V +G+G+  P++NPATG+VL  +  A+ E VD AV AA  AF +  W +T P+
Sbjct: 1   MLIGGDWVEAGDGQTMPLHNPATGEVLCVVPRATPEDVDRAVLAARQAFDDSAWTRTRPR 60

Query: 62  VRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGL 121
            R   L KLAD+++ + ++ A+LE  N GK    A   ++   +D  R+ AG A  + G 
Sbjct: 61  ERQNLLWKLADLMQRDAELLAQLECLNNGKSAAVAQVMDVQLSIDFLRYMAGWATKIEGS 120

Query: 122 AAGEYL-----EGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEI 176
           +    +     +   S IRR+ +GVV +I  WN+PL++A WKL PALA G  VVLKP++ 
Sbjct: 121 SVEVSMPLMPNDQFHSFIRREAVGVVGAIVAWNFPLLLACWKLGPALATGCTVVLKPADE 180

Query: 177 TPLTALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISH 235
           TPLTALKLAEL  +  +PAGV N++ G G T G  LT +P V  ++ TGS A G+ I   
Sbjct: 181 TPLTALKLAELVLEAGYPAGVFNVVTGTGITAGSALTHNPLVDKLTFTGSTAVGKQIGKI 240

Query: 236 TASSIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDT 295
              S+ R  +ELGGK+P IV  DAD++    G  +  ++N GQ C A  R+Y Q+  +D 
Sbjct: 241 AMESMTRVTLELGGKSPTIVMADADLKTAAAGAASAIFFNQGQVCCAGSRLYVQRKHFDN 300

Query: 296 LVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKG 355
           +V  +      +K G   D S E+GPL S    ERV   +E+ + +G    I  G ++ G
Sbjct: 301 VVADIADIANAMKLGNGLDPSVEMGPLISARQQERVYGYIEKGRESG--ATIACGGEQFG 358

Query: 356 NGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDV 415
            GY+  PT++    Q  ++VQ+E+FGPV+   PFD+E   +  ANDS YGL +S+W+ D+
Sbjct: 359 PGYFVKPTVIVDVDQQHSLVQEEIFGPVLVAIPFDDEADALRMANDSPYGLGASIWSNDL 418

Query: 416 GRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473
              HR+  R++ G  WVN H  L   +P GG K+SG G++M    +E YT ++ V++K
Sbjct: 419 AAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGYAAIEHYTELKSVLIK 476


Lambda     K      H
   0.317    0.134    0.397 

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: 593
Number of extensions: 27
Number of successful extensions: 5
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: 477
Length adjustment: 33
Effective length of query: 441
Effective length of database: 444
Effective search space:   195804
Effective search space used:   195804
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: 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 (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