GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD 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)



>FitnessBrowser__BFirm:BPHYT_RS23175
          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 (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