GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Pseudomonas fluorescens FW300-N2C3

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate AO356_06290 AO356_06290 1-pyrroline dehydrogenase

Query= BRENDA::P77674
         (474 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06290 AO356_06290
           1-pyrroline dehydrogenase
          Length = 485

 Score =  602 bits (1552), Expect = e-177
 Identities = 297/470 (63%), Positives = 358/470 (76%)

Query: 5   LLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRA 64
           LLI+GE V+GEG  +P+ NPATG+V+  +AEAS EQV+AA+ AA  AF  W +TTP+ R+
Sbjct: 12  LLIDGEFVAGEGLVEPILNPATGEVVAHVAEASTEQVEAAILAAHRAFDGWSRTTPQQRS 71

Query: 65  ECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAG 124
             LL +A  IE++    A LES NCGKPLH A  D++ A VDVFRFFAGA RC  G  +G
Sbjct: 72  NLLLDIASAIEKDADELARLESLNCGKPLHLARQDDLSATVDVFRFFAGAVRCQTGQLSG 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 GVINI+ G G+ VG  L  HPKVRMVSLTG I TG+ I+   A ++KRTH
Sbjct: 192 APALARILPRGVINIICGGGEGVGSHLVSHPKVRMVSLTGDIVTGQKILQAAAKTLKRTH 251

Query: 245 MELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAV 304
           +ELGGKAPVIV +DADI+AVVEGVRT+GYYNAGQDCTAACRIYAQ GI+D LV +LGAAV
Sbjct: 252 LELGGKAPVIVCNDADIQAVVEGVRTYGYYNAGQDCTAACRIYAQDGIHDRLVAELGAAV 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: 681
Number of extensions: 21
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 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