GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS30285
          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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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