GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Burkholderia phytofirmans PsJN

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate BPHYT_RS05370 BPHYT_RS05370 aldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__BFirm:BPHYT_RS05370
          Length = 479

 Score =  355 bits (910), Expect = e-102
 Identities = 208/481 (43%), Positives = 289/481 (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-GPWGQA 61

Query: 79  SPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKV 138
           S A+R  +L +L+ L+ A  EELA LE  DTGKP++ + R D    AR   +YA A DK+
Sbjct: 62  SAAERGRILYRLSMLVAARQEELAQLEARDTGKPLKQA-RADSAALARYFEFYAGAADKL 120

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

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

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

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

Query: 372 NAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431
            +G   A  PT+  DV  +  L+R+E+FGPVL    F+ E++AL LAN + +GL A +WT
Sbjct: 358 ESGFYQA--PTLLRDVPASHRLARDEVFGPVLAAMSFSDEDEALTLANGTPFGLVAGIWT 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: 604
Number of extensions: 33
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 (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