GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Burkholderia phytofirmans PsJN

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate BPHYT_RS23175 BPHYT_RS23175 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS23175 BPHYT_RS23175
           gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
          Length = 497

 Score =  531 bits (1369), Expect = e-155
 Identities = 269/497 (54%), Positives = 352/497 (70%), Gaps = 5/497 (1%)

Query: 1   MNFHHLAYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDID 60
           M+    A+WQDKA +L+IE R FI+GEY  A    TF+ + P+    LAK+A   + D+D
Sbjct: 1   MDKKSFAFWQDKAATLSIEGRAFIDGEYRDAEGGRTFDCLSPIDGKLLAKVADSGAADVD 60

Query: 61  RAMSAARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDD 120
            A++AAR  F+ G WS  +P +RKAVL + A  +  H +ELALLETLD GKPI  +   D
Sbjct: 61  AAVAAARRAFDSGVWSGLNPRQRKAVLLRWAASIREHMDELALLETLDAGKPIADTTSVD 120

Query: 121 IPGAARAIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGP 180
           +PGAA  + W+AEAIDK+ GEVA    H L ++ REP+GV+AA+VPWNFP+L+  WK GP
Sbjct: 121 VPGAAYCVEWFAEAIDKIGGEVAPADHHLLGLVTREPIGVVAAVVPWNFPILMASWKFGP 180

Query: 181 ALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAI 240
           ALAAGNSV+LKPSEKSPL+AIRLA LA +AG+P GV NVV G G E G+ L+ H D+D +
Sbjct: 181 ALAAGNSVVLKPSEKSPLTAIRLAQLALDAGIPAGVFNVVPGAG-EPGKLLALHQDVDCL 239

Query: 241 AFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQ 300
           AFTGST  GK +++ AG SN+KRVWLE GGKS NIV  DCPD+ +AA+A A  IFYN G+
Sbjct: 240 AFTGSTNVGKLIMQYAGQSNLKRVWLELGGKSPNIVMPDCPDMDRAANAAAGAIFYNMGE 299

Query: 301 VCIAGTRLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREG 360
           +C AG+RLL+   I D F+  L   A+++ PG+PLDP T+MG ++D    + V  +I  G
Sbjct: 300 MCTAGSRLLVHRDIKDVFIDKLIAAARSYTPGNPLDPDTSMGAIVDKVQLERVLGYIEAG 359

Query: 361 ESKGQLLLDGRNAGLAAA---IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQL 417
            ++ +LLL G           I PTIF      A ++REEIFGPVL V  F + E+A+++
Sbjct: 360 RAEAKLLLGGARVKEDTGGFYIEPTIFEIPGSGAKVAREEIFGPVLSVITFDTVEEAIRI 419

Query: 418 ANDSQYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYND-GDMTVPFGGYKQSGNGRDKS 476
           ANDS+YGL AAVWT +L+ AH +SR+L+AG+V+VN Y++ GDM  PFGGYKQSGNGRDKS
Sbjct: 420 ANDSEYGLAAAVWTSNLTTAHEVSRKLRAGTVWVNCYDEGGDMNFPFGGYKQSGNGRDKS 479

Query: 477 LHALEKFTELKTIWISL 493
           LHALEK+TELK+  + L
Sbjct: 480 LHALEKYTELKSTLVRL 496


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: 693
Number of extensions: 25
Number of successful extensions: 4
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 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, the preprint 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