GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Sinorhizobium meliloti 1021

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate SMc00880 SMc00880 oxidoreductase

Query= reanno::HerbieS:HSERO_RS05210
         (261 letters)



>FitnessBrowser__Smeli:SMc00880
          Length = 256

 Score =  236 bits (603), Expect = 3e-67
 Identities = 127/249 (51%), Positives = 164/249 (65%)

Query: 11  ASFPSLKGKRVFITGGGTGIGAAIVEAFAQQGAHVAFVDIATEASEALCNEVAAAGHPKP 70
           + FP L+ + V +TGGG+GIGAA+VEAFA+QGA VAFVDIA E+S ALC +VAA     P
Sbjct: 6   SQFPDLRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAP 65

Query: 71  LFRHCDLRDIPAFQATIAELQAQLGDFDVLVNNAANDQRHKLEEVTLEYWNDRIAINQRP 130
            F   DLR++ A +A   E  A+LG   VLVNNAA D R  LE VT E W++ +++N R 
Sbjct: 66  HFIQADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRH 125

Query: 131 SFFAVQSVVEGMKRRGGGSIINFSSISWHQSGGGFPVYTTAKASTLGLTRGLARDLGPHK 190
            FF  Q+V   M+R+GGGSI+NFSSI++  +    P Y+TAKA  +GLT+ LA  LGP  
Sbjct: 126 LFFMCQAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDN 185

Query: 191 IRVNTVTPGWVMTERQIKLWLDEEGKKAIARNQCLQGDLLPWHLARMVLFLAADDSAMCT 250
           IRVN + PG ++TERQ +LWL EE    +   QCL+  L+   L    LFLA+D SA  T
Sbjct: 186 IRVNAILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMT 245

Query: 251 AQEFIVDAG 259
           AQ  I+D G
Sbjct: 246 AQAMIIDGG 254


Lambda     K      H
   0.321    0.134    0.411 

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: 155
Number of extensions: 1
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: 261
Length of database: 256
Length adjustment: 24
Effective length of query: 237
Effective length of database: 232
Effective search space:    54984
Effective search space used:    54984
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 (21.9 bits)
S2: 47 (22.7 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