GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Burkholderia phytofirmans PsJN

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate BPHYT_RS07710 BPHYT_RS07710 succinylglutamate-semialdehyde dehydrogenase

Query= BRENDA::P76217
         (492 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS07710 BPHYT_RS07710
           succinylglutamate-semialdehyde dehydrogenase
          Length = 487

 Score =  556 bits (1434), Expect = e-163
 Identities = 270/484 (55%), Positives = 349/484 (72%)

Query: 3   LWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERH 62
           L+I+G+W  G G +    NP +G  +W+GN A A  V++A R+AR AFP W+ LS  ER 
Sbjct: 4   LFIDGEWAAGTGPAFASHNPGTGAAVWEGNSASADDVDRAVRSARRAFPAWSALSLDERC 63

Query: 63  AVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSE 122
            VV RFAAL+   K  L   I RETGKP WEA TE  +M  K+ ISI+AY+ RTGE+RS 
Sbjct: 64  GVVRRFAALVTERKEALAEAIGRETGKPLWEARTEAASMAAKVEISIQAYNERTGEKRSA 123

Query: 123 MPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMR 182
           M DG A LRHRPHGV+AVFGPYNFPGHLPNGHIVPAL+AGN ++FKPSEL P      ++
Sbjct: 124 MADGTAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNAVVFKPSELAPGVAALTVQ 183

Query: 183 LWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILAL 242
           +W+ AGLP GVLNLVQG ++TG AL+    +DGL FTGS++TG  LH+Q  G+PE +LAL
Sbjct: 184 IWRDAGLPTGVLNLVQGEKDTGIALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLAL 243

Query: 243 EMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVS 302
           EMGGNNPL+I  VAD+DAAVH TIQSAF++AGQRCTCARR+ + + A GD F+ R   V+
Sbjct: 244 EMGGNNPLVIGPVADVDAAVHHTIQSAFLSAGQRCTCARRIFVPNDAGGDRFMERFTEVT 303

Query: 303 QRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPGI 362
            R+T G ++ +PQPF+G +IS +AA ++V A ++L A G + LL           +TP I
Sbjct: 304 SRITVGEYNADPQPFMGAVISARAASRLVAAQERLLADGAKALLKMEQRDPKLGFVTPAI 363

Query: 363 IEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEA 422
           +++T V  +PDEE FGPL ++ RY +F+EA+  AN+T FGLS GL++ +   +       
Sbjct: 364 LDVTNVKNLPDEEHFGPLAQIIRYGSFNEALEQANDTEFGLSAGLLADDEALWTHFQRTI 423

Query: 423 RAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATLNP 482
           RAGIVNWN+P  GA+S APFGG G SGNHRPSA+YAADYCA+PMAS+ES  L +PA+++P
Sbjct: 424 RAGIVNWNRPTNGASSGAPFGGPGRSGNHRPSAYYAADYCAFPMASVESAQLQMPASVSP 483

Query: 483 GLDF 486
           GL F
Sbjct: 484 GLQF 487


Lambda     K      H
   0.318    0.134    0.412 

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: 778
Number of extensions: 37
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: 492
Length of database: 487
Length adjustment: 34
Effective length of query: 458
Effective length of database: 453
Effective search space:   207474
Effective search space used:   207474
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 (21.7 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, 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