Aligments for a candidate for patD in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Aligments for a candidate for patD in Pseudomonas fluorescens GW456-L13

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate PfGW456L13_3604 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= BRENDA::A0A0E3T3B5
         (503 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3604 Aldehyde
           dehydrogenase (EC 1.2.1.3)
          Length = 490

 Score =  570 bits (1470), Expect = e-167
 Identities = 276/489 (56%), Positives = 348/489 (71%), Gaps = 4/489 (0%)

Query: 9   QLFIDGEWREPVLKKRIPIINPATEQIIGDIPAATAEDVEIAVEAARKALARNKGRDWAL 68
           QL+I+GEW  P L   + +I+PATEQ    + A T EDV+ AV AAR+A        W  
Sbjct: 4   QLYINGEWVSPDLGGYLDVIDPATEQAFHRVAAGTEEDVDHAVRAARRAFDNG----WGQ 59

Query: 69  APGAVRAKYLRAIAAKIAERKSEIAKLEAIDCGKPLDEAAWDIDDVSGCFEYYADLAEGL 128
             GA R ++L A+A ++   +  +A+LE  D GKPL EA WDI D   CF YYA LA  L
Sbjct: 60  TSGAERGQWLEALADELESGQQALAELEVRDNGKPLPEAQWDIGDAIACFRYYAGLAREL 119

Query: 129 DAQQKTPISLPMEQFKSHVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCAAILKPSE 188
           D QQ  P++LP  +F   +  EPIGV G I PWNYPLLMA WKVAPALAAG   +LKPSE
Sbjct: 120 DQQQDQPLALPDARFCCRIRHEPIGVAGQIIPWNYPLLMAAWKVAPALAAGATVVLKPSE 179

Query: 189 LASVTCLELADVCREVGLPPGVLNILTGLGHEAGAPLASHPHVDKIAFTGSTMTGSKIMT 248
           L  +T LELA     +GLP GVLN++TGLG +AG+PL  HP VDK+AFTGS  TG+KIM+
Sbjct: 180 LTPLTALELAAAADRIGLPAGVLNLVTGLGADAGSPLTEHPGVDKLAFTGSVPTGAKIMS 239

Query: 249 AAAQLVKPVSLELGGKSPIVVFDDVDIDKAAEWTAFGIFWTNGQICSATSRLIIHENIAA 308
           AAA+ +K +SLELGGKS  +VFDD D++ A EW  FGIFW  GQ+CSATSRL++ E IAA
Sbjct: 240 AAARDIKNISLELGGKSAFIVFDDADVEAAVEWILFGIFWNQGQVCSATSRLLVQETIAA 299

Query: 309 KFLDRLVQWCKNIKIADPLEEGCRLGPVVSGGQYEKILKFIATAKSEGARVLSGGARPEH 368
           + ++RLV+  + I I   ++ G  LGP+VS GQY+K+L FI    + GAR+L+GG RP H
Sbjct: 300 RLIERLVEETRKISIGPGMQPGVLLGPLVSQGQYDKVLGFIDQGLASGARLLTGGRRPAH 359

Query: 369 LKKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFSSEDEALELANDSHYGLGAAVISK 428
           L++G+F+EP I  +   S  +WREEVFGPVLC+K F +E++AL++AN S +GL AAV+S 
Sbjct: 360 LREGYFVEPAIFDEPGHSSILWREEVFGPVLCIKRFKTEEQALQMANASRFGLAAAVMSA 419

Query: 429 DLERCERVSKALQAGIVWINCSQPCFCQAPWGGNKRSGFGRELGKWGLDNYLTVKQVTEY 488
           DL+R  RV+  L+AGIVW+NCSQP F +APWGG K SG GRELG+WGL NYL VKQVTEY
Sbjct: 420 DLQRTARVANQLRAGIVWVNCSQPTFVEAPWGGMKHSGIGRELGQWGLHNYLEVKQVTEY 479

Query: 489 VSDDPWGWY 497
           VSD PWGWY
Sbjct: 480 VSDQPWGWY 488


Lambda     K      H
   0.319    0.136    0.419 

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: 754
Number of extensions: 23
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: 503
Length of database: 490
Length adjustment: 34
Effective length of query: 469
Effective length of database: 456
Effective search space:   213864
Effective search space used:   213864
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources