GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Burkholderia phytofirmans PsJN

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate BPHYT_RS23175 BPHYT_RS23175 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

Query= BRENDA::Q83XU8
         (485 letters)



>FitnessBrowser__BFirm:BPHYT_RS23175
          Length = 497

 Score =  327 bits (839), Expect = 4e-94
 Identities = 190/466 (40%), Positives = 267/466 (57%), Gaps = 14/466 (3%)

Query: 24  SPLNNAVIAKVHEAGRAEVDAAVAAAQAAL-KGAWGRMSLAQRVEVLYAVADGINRRFDD 82
           SP++  ++AKV ++G A+VDAAVAAA+ A   G W  ++  QR  VL   A  I    D+
Sbjct: 41  SPIDGKLLAKVADSGAADVDAAVAAARRAFDSGVWSGLNPRQRKAVLLRWAASIREHMDE 100

Query: 83  FLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRR 142
               E  D GKP++    VD+P  A   + FA+ +  +  E      P     +    R 
Sbjct: 101 LALLETLDAGKPIADTTSVDVPGAAYCVEWFAEAIDKIGGEV----APADHHLLGLVTRE 156

Query: 143 PVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGV 202
           P+GVV  + PWN P+L+ +WK GPALA GN+VV+KPSE++P TA  L ++   AG+P GV
Sbjct: 157 PIGVVAAVVPWNFPILMASWKFGPALAAGNSVVLKPSEKSPLTAIRLAQLALDAGIPAGV 216

Query: 203 YNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMK-AAADGARPVSLELGGKNAAI 261
           +NVV G G    G+ L  H DV+ + FTG T  G+ IM+ A     + V LELGGK+  I
Sbjct: 217 FNVVPGAG--EPGKLLALHQDVDCLAFTGSTNVGKLIMQYAGQSNLKRVWLELGGKSPNI 274

Query: 262 VFADC-DLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPE 320
           V  DC D+D+A      + F N G++C    R+ V R I D F+ +L   A     G P 
Sbjct: 275 VMPDCPDMDRAANAAAGAIFYNMGEMCTAGSRLLVHRDIKDVFIDKLIAAARSYTPGNPL 334

Query: 321 DLATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLG 380
           D  T MG ++ +   E+VL Y  +A  A A ++ GG      +   GG +++PTI+   G
Sbjct: 335 DPDTSMGAIVDKVQLERVLGYI-EAGRAEAKLLLGGA---RVKEDTGGFYIEPTIFEIPG 390

Query: 381 DDSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGI 440
             + VAREEIFGP   V+ FD+ EE IR AND++YGLA  +WT+NL+ AH V+  +  G 
Sbjct: 391 SGAKVAREEIFGPVLSVITFDTVEEAIRIANDSEYGLAAAVWTSNLTTAHEVSRKLRAGT 450

Query: 441 AWVNSWFL-RDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485
            WVN +    D+   FGG KQSG GR+  +H+LE YTELK+  ++L
Sbjct: 451 VWVNCYDEGGDMNFPFGGYKQSGNGRDKSLHALEKYTELKSTLVRL 496


Lambda     K      H
   0.318    0.135    0.406 

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: 565
Number of extensions: 39
Number of successful extensions: 8
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: 485
Length of database: 497
Length adjustment: 34
Effective length of query: 451
Effective length of database: 463
Effective search space:   208813
Effective search space used:   208813
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