GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28685
          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 (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