GapMind for catabolism of small carbon sources

 

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

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate AO356_28685 AO356_28685 betaine-aldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28685 AO356_28685
           betaine-aldehyde dehydrogenase
          Length = 496

 Score =  392 bits (1006), Expect = e-113
 Identities = 220/486 (45%), Positives = 304/486 (62%), Gaps = 12/486 (2%)

Query: 16  LAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDW 75
           L+   RLFI G +  AA    F   +P T+  LA++A G   D+D A++AAR  F  G W
Sbjct: 14  LSQPGRLFIGGTWQDAANGRRFAVENPATEHTLAEVAEGGERDVDAAVAAARAAFT-GTW 72

Query: 76  SLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAI 135
           +  SPA+R  +L +LA+L++ H EELA L TL+ GKPI  + R +   AA  IR++A   
Sbjct: 73  AQQSPAQRGLLLFRLAELLDQHREELAQLITLENGKPIG-AARGEAASAANIIRYFAGWP 131

Query: 136 DKVYGEVATTSSHE----LAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILK 191
            K+ G     S       L   +REPVGV A IVPWNFPL +  WKLGP LA G   +LK
Sbjct: 132 TKIEGSTLPVSPSSGAPMLNYTLREPVGVCALIVPWNFPLTMCVWKLGPVLATGCVAVLK 191

Query: 192 PSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQ 251
           P+E++PL AIRL  L + AG P GV+N++TG G + G  L++H D+D IAFTGST+ G+ 
Sbjct: 192 PAEQTPLVAIRLVQLIEAAGFPAGVVNLLTGLGAQTGAPLAQHPDVDKIAFTGSTQVGR- 250

Query: 252 LLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLE 311
           L+  A   NMK+V LE GGKS NI+  D  D+ +AA   A GIFYNQGQVC AG+RL + 
Sbjct: 251 LIAQAATGNMKKVSLELGGKSPNIILPDA-DIVRAAKGAADGIFYNQGQVCTAGSRLYVH 309

Query: 312 ESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDG- 370
            S+ D+ L  L++ A     G  LDPA++MG L+      +V  +++ G+ +G  L+ G 
Sbjct: 310 ASVLDQVLEELQRHAAAHVLGPGLDPASSMGPLVSARQLGTVRGYLQRGQEEGAELICGG 369

Query: 371 -RNAGLAAA--IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGA 427
            R A L     I P++F+D    A ++REEIFGPVL V  +T  ++ +  ANDS YGL A
Sbjct: 370 DRPAHLERGHFIRPSVFLDRAERACVAREEIFGPVLTVMSWTEIDELVLRANDSPYGLAA 429

Query: 428 AVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELK 487
            +WTRDL  AHR++ +LKAGSV++N +N  D   PFGGYKQSG GR+   + ++ +TE K
Sbjct: 430 GLWTRDLRSAHRVAAQLKAGSVWINCWNVVDPASPFGGYKQSGWGREMGKNVIDAYTETK 489

Query: 488 TIWISL 493
           ++++ L
Sbjct: 490 SVYVDL 495


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: 647
Number of extensions: 32
Number of successful extensions: 6
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: 496
Length adjustment: 34
Effective length of query: 461
Effective length of database: 462
Effective search space:   212982
Effective search space used:   212982
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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