GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Pseudomonas fluorescens FW300-N2E2

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Pf6N2E2_3126 4-aminobutyraldehyde dehydrogenase (EC 1.2.1.19)

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3126
          Length = 485

 Score =  599 bits (1545), Expect = e-176
 Identities = 298/470 (63%), Positives = 356/470 (75%)

Query: 5   LLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRA 64
           LLI+GELV G G  +P+ NPATG+V+  IAEAS EQV+AA+ AA  AF  W +TTP+ R+
Sbjct: 12  LLIDGELVPGAGIVEPILNPATGEVVAHIAEASTEQVEAAILAAHRAFDGWSRTTPQQRS 71

Query: 65  ECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAG 124
             LL +A  IE+N    A LES NCGKPL+ A  D++ A VDVFRFFAGA RC  G  +G
Sbjct: 72  NLLLDIASAIEKNADELARLESLNCGKPLYLARQDDLSATVDVFRFFAGAVRCQTGQLSG 131

Query: 125 EYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKL 184
           EYL G+TSM+RRDP+GVVASIAPWNYP+MMAAWK+APALAAGN +V KPSE TPL+ L L
Sbjct: 132 EYLPGYTSMVRRDPIGVVASIAPWNYPIMMAAWKIAPALAAGNTLVFKPSEHTPLSILAL 191

Query: 185 AELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTH 244
           A     I P GVINIL G G+ VG  L  HPKVRMVSLTG I TG+ I+   A ++KRTH
Sbjct: 192 APTLAQILPRGVINILCGGGEGVGSHLVSHPKVRMVSLTGDIVTGQKILQAAAKTLKRTH 251

Query: 245 MELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAV 304
           +ELGGKAPVIV +DADI+AVVEGVRT+GYYNAGQDCTAACRIYAQ  I+D LV +LGAAV
Sbjct: 252 LELGGKAPVIVCNDADIQAVVEGVRTYGYYNAGQDCTAACRIYAQGAIHDRLVAELGAAV 311

Query: 305 ATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTL 364
           ++L+     D   E+GPL S    +RV   VE A    HI+ ITG     G G+YY PTL
Sbjct: 312 SSLRFAGKRDADNEIGPLISTRQRDRVASFVERALGQPHIERITGAAVHSGAGFYYQPTL 371

Query: 365 LAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSAR 424
           LAG  Q D IVQ+EVFGPVV+VT FD   Q V+WANDS+YGLASSVWT+++ +A +V+AR
Sbjct: 372 LAGCKQSDEIVQREVFGPVVTVTRFDELSQAVDWANDSEYGLASSVWTQNLDKAMQVAAR 431

Query: 425 LQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474
           LQYGCTW+N+HFMLVSEMPHGG K SGYGKD+S   L+DY+VVRH+M +H
Sbjct: 432 LQYGCTWINSHFMLVSEMPHGGLKRSGYGKDLSSDSLQDYSVVRHIMARH 481


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: 672
Number of extensions: 19
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: 474
Length of database: 485
Length adjustment: 34
Effective length of query: 440
Effective length of database: 451
Effective search space:   198440
Effective search space used:   198440
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