GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Burkholderia phytofirmans PsJN

Align succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized)
to candidate BPHYT_RS34305 BPHYT_RS34305 succinate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-20455
         (480 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS34305 BPHYT_RS34305
           succinate-semialdehyde dehydrogenase
          Length = 479

 Score =  612 bits (1578), Expect = e-180
 Identities = 298/468 (63%), Positives = 365/468 (77%), Gaps = 2/468 (0%)

Query: 12  YINGEWLSALGGETQSIFNPATGQLIGTVPMMGRQEARQAIAAANQALPAWRALPAKERS 71
           +I GEW    G +T ++ NPATG+++  V   G  E  QAIAAA +A PAWRAL AKERS
Sbjct: 10  FIGGEWYE--GADTYAVLNPATGEVVAHVAKGGAAETAQAIAAAERAFPAWRALTAKERS 67

Query: 72  ARLRAWFELMLEHQEELARLMTIEQGKPLAEARNEILYAASFVEWFAEEGKRVYGDVIPS 131
           AR++ W ELMLE+++ LA L+T+EQGKPLAEAR E+ YAASF EWFAEE KR YGDVIPS
Sbjct: 68  ARVKRWGELMLENRDALAELLTLEQGKPLAEARGEVGYAASFFEWFAEEAKRAYGDVIPS 127

Query: 132 PQADKRLLVIKQPVGVTAAITPWNFPSAMITRKAAPALAAGCTMVLKPAPQTPFSALALA 191
           P  + +++V ++PVGV AAITPWNFP AMITRKA PALAAGCTMVLKP+ +TP SA ALA
Sbjct: 128 PNPNAKIIVTREPVGVVAAITPWNFPLAMITRKAGPALAAGCTMVLKPSEETPLSAFALA 187

Query: 192 ALAQRAGIPAGVFNVVTGSAQEIGGEFTGNPIVRKLTFTGSTHIGRLLMAQCAHDVKKMS 251
            LA +AGIP GVFN+V+G A  IGG  T + +VRKL+FTGST +G+LL  Q A  +KK+S
Sbjct: 188 VLAAKAGIPPGVFNIVSGDAVAIGGALTESDVVRKLSFTGSTRVGKLLAKQSADTLKKLS 247

Query: 252 LELGGNAPFIVFEDADLDKAAEGALIAKYRNNGQTCVCTNRIYVHDSVHDAFAGKLKKAV 311
           LELGGNAPFIVF+DADLD A +GA+ +K+RN GQTCVC NR YV D ++DAF   L +AV
Sbjct: 248 LELGGNAPFIVFDDADLDAAVQGAMASKFRNTGQTCVCVNRFYVQDGIYDAFTSALTQAV 307

Query: 312 EGLRVGNGLEDGVTVGPLINDAAVQKVRSHIADAVGKGASILAGGKPHALGGTFFEPTIL 371
             +RVGN L+  V  GPLIN AA++KV +H+ADA+ KGA IL GGKPH LGGTF+EPT+L
Sbjct: 308 RKMRVGNALQGEVEQGPLINQAALKKVETHVADALQKGAKILTGGKPHTLGGTFYEPTVL 367

Query: 372 ANVPHDALVAHEETFGPLAPLFRFRDEAEVVGRANDTEYGLAAYFYTENLGRIFRVAEAL 431
           A+  +  L+A EETFGP+A  FRF+ EAE +  ANDT +GL+AYFYT +L R +RV EAL
Sbjct: 368 ADADNSMLIAGEETFGPVAACFRFKTEAEAIEAANDTPFGLSAYFYTRDLARAWRVGEAL 427

Query: 432 EYGMVGINCGAISNEVAPFGGVKASGLGREGSKYGIEEYLEIKYLSLG 479
           E GMVGIN G +S EVAPFGGVK SGLGREGSKYG++EY E+KY+ +G
Sbjct: 428 ESGMVGINEGIVSTEVAPFGGVKQSGLGREGSKYGLDEYTELKYMMMG 475


Lambda     K      H
   0.319    0.135    0.399 

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: 701
Number of extensions: 20
Number of successful extensions: 1
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: 480
Length of database: 479
Length adjustment: 34
Effective length of query: 446
Effective length of database: 445
Effective search space:   198470
Effective search space used:   198470
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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