GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3604
          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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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