Aligments for a candidate for gabD in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments for a candidate for gabD in Burkholderia phytofirmans PsJN

Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate BPHYT_RS30285 BPHYT_RS30285 succinate-semialdehyde dehydrogenase

Query= BRENDA::P25526
         (482 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS30285 BPHYT_RS30285
           succinate-semialdehyde dehydrogenase
          Length = 490

 Score =  541 bits (1393), Expect = e-158
 Identities = 271/486 (55%), Positives = 347/486 (71%), Gaps = 6/486 (1%)

Query: 1   MKLNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRA 60
           + L  + L R Q LI+G W  A +G    VTNPA G+ +  V   GA + RAA DAA RA
Sbjct: 3   LALTRNELIRPQNLIDGAWTGAADGARFAVTNPATGETIVEVADSGAADARAATDAAARA 62

Query: 61  LPAWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFA 120
            PAWR    +ERA ILR W  L++ + DDLA+LM++EQGKPLAEA+GE++Y AS++ WFA
Sbjct: 63  FPAWRDTLPRERAEILRRWHALIVANTDDLAKLMSMEQGKPLAEARGEVAYGASYVAWFA 122

Query: 121 EEGKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180
           +E  RIYGD IP  Q  KR+  +K+P+GV AAITPWNFP AMI RK  PALAAGCT+V K
Sbjct: 123 DEATRIYGDLIPQQQRGKRMSAVKEPVGVIAAITPWNFPLAMIARKIAPALAAGCTVVAK 182

Query: 181 PASQTPFSALALAELAIRAGVPAGVFNVVTGS----AGAVGNELTSNPLVRKLSFTGSTE 236
           PA  TP +ALALA LA  AG+P GV N+++ S      AV + L ++  VRK++FTGST 
Sbjct: 183 PAEDTPLTALALAVLAQEAGLPDGVLNMLSASREQGIAAVADWL-ADSRVRKITFTGSTP 241

Query: 237 IGRQLMEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLY 296
           +G+ L  + A  +KK+SLELGGNAPFIVFDDADLD AV G +A+KFRN GQTCVC NR+Y
Sbjct: 242 VGKHLARESAGTLKKLSLELGGNAPFIVFDDADLDAAVTGLMAAKFRNGGQTCVCPNRVY 301

Query: 297 VQDGVYDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVC 356
           VQ GVY+RFA+ L + V  L +    D    IGP+I+E+A+ K+  H+ DA++ GA+V+ 
Sbjct: 302 VQAGVYERFADLLAKRVGALKVAPATDPQAQIGPMINERAIQKIARHVEDAVKHGAKVLV 361

Query: 357 GGK-AHERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLA 415
           GGK   E G N++ PT+L D   +  VS EETFGP+APLFRF +EA+ I  +NDT FGLA
Sbjct: 362 GGKRLTELGPNYYAPTVLTDARDDMLVSCEETFGPVAPLFRFNEEAEAIRLSNDTPFGLA 421

Query: 416 AYFYARDLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEI 475
           AYFY +D+ R+ RV   LE G++GIN G +S+E APFGG+K SG GREGSKYG++DY+ I
Sbjct: 422 AYFYTQDVRRINRVAAQLEAGVIGINEGAVSSEAAPFGGVKESGYGREGSKYGLDDYMSI 481

Query: 476 KYMCIG 481
           KYMC G
Sbjct: 482 KYMCQG 487


Lambda     K      H
   0.318    0.135    0.395 

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: 675
Number of extensions: 18
Number of successful extensions: 3
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: 482
Length of database: 490
Length adjustment: 34
Effective length of query: 448
Effective length of database: 456
Effective search space:   204288
Effective search space used:   204288
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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources