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_2417 Betaine aldehyde dehydrogenase (EC 1.2.1.8)

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2417
          Length = 490

 Score =  321 bits (823), Expect = 3e-92
 Identities = 174/460 (37%), Positives = 266/460 (57%), Gaps = 14/460 (3%)

Query: 23  NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82
           NPA G+VL  +  A+ E V+ AV +A+     W   T   R+  L +  D++ E     A
Sbjct: 28  NPANGEVLATVQRATKEDVERAVVSAEKGQKIWAAMTAMERSRILRRAVDILRERNDELA 87

Query: 83  ELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMI---RRDPL 139
            LE+ + GK        +I    DV  ++AG    + G    E +   T+     RR+PL
Sbjct: 88  ALETLDTGKAYSETRYVDIVTGADVLEYYAGLVPAIEG----EQIPLRTTSFVYTRREPL 143

Query: 140 GVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDI-FPAGVIN 198
           G+VA I  WNYP+ +A WK APALAAGN ++ KPSE+T LT LKLAE+  +   PAGV N
Sbjct: 144 GIVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTTLKLAEIYTEAGLPAGVFN 203

Query: 199 ILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHII-SHTASSIKRTHMELGGKAPVIVFD 257
           +L G G+ VG  LT HP++  +S TG   TG+ ++ S + SS+K   MELGGK+P+I+FD
Sbjct: 204 VLTGSGREVGTWLTEHPRIEKISFTGGTDTGKKVMASASGSSLKDVTMELGGKSPLIIFD 263

Query: 258 DADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDEST 317
           DAD++   +      +Y++GQ CT   R++    +      K+   VA ++ G P+DE+T
Sbjct: 264 DADLDRAADTAMMANFYSSGQVCTNGTRVFVPSHLKAAFEAKIVERVARIRVGNPEDENT 323

Query: 318 ELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRK----GNGYYYAPTLLAGALQDDA 373
             GPL S AH+E V   + + K  G  +++ GG++        G + APT+      +  
Sbjct: 324 NFGPLVSFAHMESVLGYIAKGKEEG-ARLLCGGDRLTDGEFAKGAFVAPTVFTDCTDEMT 382

Query: 374 IVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVN 433
           IV++E+FGPV+S+  ++ EE+V+  AND+++GLA+ V TKD+ RAHRV  +L+ G  W+N
Sbjct: 383 IVREEIFGPVMSILTYETEEEVIRRANDTEFGLAAGVVTKDLNRAHRVIHQLEAGICWIN 442

Query: 434 THFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473
                 ++MP GG K SG G++  +  L ++T ++ V V+
Sbjct: 443 AWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIKSVQVE 482


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: 556
Number of extensions: 24
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: 490
Length adjustment: 34
Effective length of query: 440
Effective length of database: 456
Effective search space:   200640
Effective search space used:   200640
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: 52 (24.6 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