GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Herbaspirillum seropedicae SmR1

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate HSERO_RS13590 HSERO_RS13590 D-galactose-1-dehydrogenase

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



>FitnessBrowser__HerbieS:HSERO_RS13590
          Length = 307

 Score =  384 bits (987), Expect = e-111
 Identities = 186/306 (60%), Positives = 231/306 (75%)

Query: 1   MSPINIAIVGVGKIVRDQHLPALAKNADYRLIAAASRHGTVDGIDNFKSIEAMIDAVPAV 60
           M+ I +AI GVGKIV DQH PA+A N D++L+A ASR+ ++DG+  +KS+  M+ +  A+
Sbjct: 1   MTAIQLAIAGVGKIVYDQHAPAIAGNTDFKLVATASRNHSIDGVTAYKSMAEMLASGTAI 60

Query: 61  EAVSLCMPPQYRYEAARTALAAGKHVFLEKPPGATLSEVADLEALAEEKGVSLFASWHSR 120
           +A+SLCMPPQYRYEAAR A+ AGKHVFLEKPPGATLSEV  L  LA E+GV+LFASWHSR
Sbjct: 61  DAISLCMPPQYRYEAAREAIRAGKHVFLEKPPGATLSEVESLRDLAAEQGVTLFASWHSR 120

Query: 121 YAPAVEAAKTFLASAAIRNVRIIWKEDVRHWHPNQEWIWAAGGLGVFDPGINALSIMTHI 180
           +APAV+  K  L   A R V++IW+EDVRHWHP+QEWIW  GGLGVFDPGINALSI+T I
Sbjct: 121 HAPAVQVVKRHLQQHAPRQVKVIWREDVRHWHPDQEWIWQPGGLGVFDPGINALSIVTEI 180

Query: 181 LPRPVFITSATLEFPENRDAPIAATIAFSDAEKLDVAAEFDWRQTGKQSWDIVAETDAGG 240
           LP+ +F+  A LE P NR  PIAA +AF+DA   DV A+FDWRQTG Q+WDI+ ET +  
Sbjct: 181 LPQAMFLKQAALEVPSNRQTPIAARLAFTDALGTDVQADFDWRQTGGQTWDIIIETGSTH 240

Query: 241 MVLSEGGAKLAIDGKIVHEEPEQEYPMLYRRFAEIIKAGRSDVDLAPLRHVADAFMLGRR 300
           + L +GG +L IDGK      E EYP LY+ F ++I+   SDVD+APLRHVADAFMLG  
Sbjct: 241 VHLKKGGHELWIDGKQSELPVEGEYPSLYQHFCQLIRKHASDVDVAPLRHVADAFMLGEH 300

Query: 301 KFVEAF 306
              +AF
Sbjct: 301 IVTDAF 306


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: 369
Number of extensions: 8
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: 308
Length of database: 307
Length adjustment: 27
Effective length of query: 281
Effective length of database: 280
Effective search space:    78680
Effective search space used:    78680
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 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