GapMind for catabolism of small carbon sources

 

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

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate PfGW456L13_805 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_805
          Length = 497

 Score =  569 bits (1466), Expect = e-167
 Identities = 284/491 (57%), Positives = 353/491 (71%), Gaps = 4/491 (0%)

Query: 7   AYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAA 66
           A W+ +A  L IE R +INGEYT A   ETFE + PV    L KIA   + D  RA+  A
Sbjct: 7   ADWEQRARDLKIEGRAYINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQRAVENA 66

Query: 67  RGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAAR 126
           R  F  G WS  +P KRK+ + + A L++ HAEELALLETLD GKPI  SL  D+PGAA+
Sbjct: 67  RATFNSGVWSRLAPTKRKSTMIRFAGLLKQHAEELALLETLDMGKPISDSLYIDVPGAAQ 126

Query: 127 AIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGN 186
           A+ W  EAIDK+Y EVA T   +L ++ REPVGV+ AIVPWNFPL++ CWKLGPAL+ GN
Sbjct: 127 ALSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGN 186

Query: 187 SVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGST 246
           SVILKPSEKSPL+AIR+A LA EAG+P GVLNV+ G+GH  G+AL+ HND+D + FTGST
Sbjct: 187 SVILKPSEKSPLTAIRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTLVFTGST 246

Query: 247 RTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGT 306
           +  KQLL  +G+SNMKRVWLEAGGKS NIVFAD P+LQ AA A A  I +NQG+VC AG+
Sbjct: 247 KIAKQLLIYSGESNMKRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGEVCTAGS 306

Query: 307 RLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQL 366
           RLL+E SI D+FL L+ +  + W+PG+PLDPAT +G L+D    ++V S+I  G + G  
Sbjct: 307 RLLVERSIKDKFLPLVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESGHADGAR 366

Query: 367 LLDGRNAGLAAAIG----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQ 422
           L+ G    L    G    PTIF  V     +++EEIFGPVL V  F S E+A+ +AND+ 
Sbjct: 367 LVAGGKRTLQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIAIANDTP 426

Query: 423 YGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEK 482
           YGL AAVWT D+S+AH  +R L+AGSV+VN Y+ GDMT PFGG+KQSGNGRDKSLHA +K
Sbjct: 427 YGLAAAVWTADISKAHLTARALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDK 486

Query: 483 FTELKTIWISL 493
           +TELK  WI L
Sbjct: 487 YTELKATWIKL 497


Lambda     K      H
   0.317    0.133    0.389 

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: 646
Number of extensions: 26
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: 495
Length of database: 497
Length adjustment: 34
Effective length of query: 461
Effective length of database: 463
Effective search space:   213443
Effective search space used:   213443
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