GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuC in Paraburkholderia bryophila 376MFSha3.1

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate H281DRAFT_00213 H281DRAFT_00213 aldehyde dehydrogenase (NAD+)

Query= BRENDA::P23883
         (495 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00213 H281DRAFT_00213
           aldehyde dehydrogenase (NAD+)
          Length = 479

 Score =  358 bits (920), Expect = e-103
 Identities = 209/481 (43%), Positives = 291/481 (60%), Gaps = 15/481 (3%)

Query: 19  ENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLS 78
           E R FI GE++AA+  ET   +DP    P  ++ARG + DID A+ AAR  FE G W  +
Sbjct: 3   EARHFIGGEWSAASGGETIAVLDPSDGQPFTQLARGTAADIDAAVHAARRAFE-GAWGAA 61

Query: 79  SPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKV 138
           S A+R  VL +L+ L+ A  EELA LE  DTGKP++ + R D     R   +YA A DK+
Sbjct: 62  SAAERGRVLYRLSMLVAARQEELAQLEARDTGKPLKQA-RADSAALVRYFEFYAGAADKL 120

Query: 139 YGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPL 198
           +GE     +    M +REP GV   IVPWN+P+ +    +G ALA GN+ ++KP+E + L
Sbjct: 121 HGETLPYQAGYTVMTIREPHGVTGHIVPWNYPMQIFGRSVGAALAVGNACVVKPAEDACL 180

Query: 199 SAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGD 258
           S +R+A LA EAGLP G LN+VTG+GHEAG AL+RH+ ID I+FTGS  TGK + + A +
Sbjct: 181 SVLRVAELAAEAGLPAGALNIVTGYGHEAGAALARHSGIDHISFTGSPETGKLVTQMAAE 240

Query: 259 SNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEF 318
           +++  V LE GGKS  +VFAD  DL  A     + I  N GQ C AG+R+L++ +I +  
Sbjct: 241 NHVP-VTLELGGKSPQLVFADA-DLDAALPVLVSAIVQNAGQTCSAGSRVLIDRAIYEPL 298

Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGE-------SKGQLLLDGR 371
           L  L       + G P       G LI+      V  F+ + +       + G+++ +  
Sbjct: 299 LDRLSSAFNALRVG-PSHADLDCGPLINAKQQRRVWDFLSDAQHDGIAMAAHGEVIPEAP 357

Query: 372 NAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431
            +G   A  PT+  DV  +  L+R+E+FGPVL    F+ E++AL LAN +QYGL A +WT
Sbjct: 358 ESGFYQA--PTLLRDVPASHRLARDEVFGPVLAAMSFSDEDEALALANGTQYGLVAGIWT 415

Query: 432 RDLSRAHRMSRRLKAGSVFVNNYN-DGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIW 490
           RD +R  R++RRL++G VF+NNY   G + +PFGG K SG+GR+K   AL  FT LKTI 
Sbjct: 416 RDGARQMRLARRLRSGQVFINNYGAGGGVELPFGGVKHSGHGREKGFEALYGFTALKTIA 475

Query: 491 I 491
           I
Sbjct: 476 I 476


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: 607
Number of extensions: 34
Number of successful extensions: 7
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: 479
Length adjustment: 34
Effective length of query: 461
Effective length of database: 445
Effective search space:   205145
Effective search space used:   205145
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