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_059153417.1 V474_RS22305 Gfo/Idh/MocA family oxidoreductase

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



>NCBI__GCF_001046635.1:WP_059153417.1
          Length = 306

 Score =  318 bits (814), Expect = 1e-91
 Identities = 160/306 (52%), Positives = 205/306 (66%), Gaps = 2/306 (0%)

Query: 1   MSPINIAIVGVGKIVRDQHLPALAKNADYRLIAAASRHGTVDGIDNFKSIEAMIDAVPAV 60
           M P+ + +VG+GKI RDQH PA+A N    L+A ASRHG +DG+D +  I  M+ A  A+
Sbjct: 1   MEPVRLGLVGIGKIARDQHFPAIAGNDRLNLVATASRHGRLDGVDGYHDIAEMVSAT-AL 59

Query: 61  EAVSLCMPPQYRYEAARTALAAGKHVFLEKPPGATLSEVADLEALAEEKGVSLFASWHSR 120
           +AVSLC PP  RYE A  A+ AG HV LEKPP  TLS V  L A A + GVSLFA+WHSR
Sbjct: 60  DAVSLCTPPDGRYEQALIAIEAGVHVMLEKPPAVTLSHVEALVAAARKAGVSLFATWHSR 119

Query: 121 YAPAVEAAKTFLASAAIRNVRIIWKEDVRHWHPNQEWIWAAGGLGVFDPGINALSIMTHI 180
            A  V  A+ +LA   I  VRI WKED+R WHP QEWI   GG GVFDPGINALSI T I
Sbjct: 120 EAAGVAPARAWLADKRIDAVRIDWKEDIRRWHPGQEWILGPGGFGVFDPGINALSIATEI 179

Query: 181 LPRPVFITSATLEFPENRDAPIAATIAFSDAEKLDVAAEFDWRQTGKQSWDIVAETDAGG 240
           LPR +F+ SA+++ PE R +P+AA+I        +V AEFD+ QTG Q+W I  +TDAG 
Sbjct: 180 LPRELFVESASMDVPEGRASPLAASILMR-CGSAEVRAEFDFLQTGPQTWSIEVDTDAGT 238

Query: 241 MVLSEGGAKLAIDGKIVHEEPEQEYPMLYRRFAEIIKAGRSDVDLAPLRHVADAFMLGRR 300
           + L++GG+ + + G+     P++EY  LY RFA+++     DVDL PLR VADAF++  R
Sbjct: 239 LRLTQGGSVIQLPGEAEQTAPDEEYARLYDRFADLVAERAIDVDLRPLRLVADAFLIADR 298

Query: 301 KFVEAF 306
           +  EAF
Sbjct: 299 RVTEAF 304


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: 308
Number of extensions: 19
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: 306
Length adjustment: 27
Effective length of query: 281
Effective length of database: 279
Effective search space:    78399
Effective search space used:    78399
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