GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Novosphingobium barchaimii LL02

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_059153651.1 V474_RS23770 Gfo/Idh/MocA family oxidoreductase

Query= reanno::Smeli:SMc00588
         (308 letters)



>NCBI__GCF_001046635.1:WP_059153651.1
          Length = 308

 Score =  369 bits (948), Expect = e-107
 Identities = 185/309 (59%), Positives = 223/309 (72%), Gaps = 2/309 (0%)

Query: 1   MSPINIAIVGVGKIVRDQHLPALAKNADYRLIAAASRHGT-VDGIDNFKSIEAMIDAVPA 59
           M PI IA+VGVGKI RDQHLPA+A N  + L A  S H   V+G+ + KS++ +I+  PA
Sbjct: 1   MDPIRIAVVGVGKIARDQHLPAIAGNKAFSLAATVSPHDAGVEGVSHHKSLDELIENGPA 60

Query: 60  VEAVSLCMPPQYRYEAARTALAAGKHVFLEKPPGATLSEVADLEALAEEKGVSLFASWHS 119
           V+AV+LC PPQ RY+ A  AL  G HVFLEKPPGATLSE   L + AE+ G +LFA+WHS
Sbjct: 61  VDAVALCTPPQVRYDLAVQALNKGMHVFLEKPPGATLSECVALSSRAEKVGTTLFAAWHS 120

Query: 120 RYAPAVEAAKTFLASAAIRNVRIIWKEDVRHWHPNQEWIWAAGGLGVFDPGINALSIMTH 179
           R+A  V  A+ +LA   I +V+I+W+EDVR WHP Q WIW  GGLGVFDPGINALSI+TH
Sbjct: 121 RFAAGVAPARAWLAERRIESVKIVWREDVRVWHPGQAWIWEPGGLGVFDPGINALSILTH 180

Query: 180 ILPRPVFITSATLEFPENRDAPIAATIAFSDAEKLDVAAEFDWRQTGKQSWDIVAETDAG 239
           ILPRPVF+ +ATLE P NR APIAA I F D     +  + DWRQTG QSWDIV ETDAG
Sbjct: 181 ILPRPVFLKTATLEIPANRAAPIAADIQFRDTAGAPIHMDLDWRQTGPQSWDIVVETDAG 240

Query: 240 GMVLSEGGAKLAIDGKIVHEEPEQEYPMLYRRFAEIIKAGRSDVDLAPLRHVADAFMLGR 299
            + LS GGA L +     H E + EYP LY RFA +I+ GRSDVD+APLR VADAF+ G 
Sbjct: 241 TLKLSNGGAVLTLPTGAEHSE-DLEYPGLYARFANLIRGGRSDVDIAPLRLVADAFLRGN 299

Query: 300 RKFVEAFHD 308
           R+ V+AFHD
Sbjct: 300 RQTVDAFHD 308


Lambda     K      H
   0.320    0.134    0.405 

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: 338
Number of extensions: 16
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: 308
Length of database: 308
Length adjustment: 27
Effective length of query: 281
Effective length of database: 281
Effective search space:    78961
Effective search space used:    78961
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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