GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS07710
          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 (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