GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacD in Sinorhizobium meliloti 1021

Align D-xylonate dehydratase subunit (EC 4.2.1.25; EC 4.2.1.82) (characterized)
to candidate SM_b20510 SM_b20510 galactonate dehydratase

Query= metacyc::MONOMER-18070
         (393 letters)



>FitnessBrowser__Smeli:SM_b20510
          Length = 382

 Score =  203 bits (517), Expect = 6e-57
 Identities = 130/387 (33%), Positives = 209/387 (54%), Gaps = 21/387 (5%)

Query: 3   KISEIEAYILGKEVTSAQWASLMVLVRVTTNDGRVGWGETVSALRAEAVANFVKKINTVL 62
           KI+++  YI+       +W    + +++ T++G VGWGE V   RA  V   V +++  L
Sbjct: 2   KITKLTTYIV-----PPRW----LFLKIETDEGVVGWGEPVVEGRALTVEAAVHELSDYL 52

Query: 63  KGNDVFNVEKNRLEWYKHDFNMTISLESTTAYSAVDIASWDIIGKELGAPLYKLLGGKTR 122
            G D F +E +    Y+  F    ++  + A + +D A WDI GK LG P++ LLGG+ R
Sbjct: 53  VGKDPFLIEDHWNVLYRGGFYRGGAIHMS-ALAGIDQALWDIKGKALGQPVHSLLGGQCR 111

Query: 123 DKVLVYANGWYQNCVKPEDFAEKAKEIVKMGYKALKFDPFGPYFNDISKKGLDIAEERVK 182
           D++ VY+  W     +P D A  A+E+V  G+KA+K +         + + +D A E + 
Sbjct: 112 DRIKVYS--WIGGD-RPSDVANNAREVVARGFKAIKLNGCEEMQIVDTNEKIDKAVETIG 168

Query: 183 AVREAVGDNVDILIEHHGRFNANSAIMIAKRLEKYNPLFMEEPIHPEDVEGLRKYRNNTS 242
            +R+A+G +V I ++ HGR +   A ++AK LE +  +F+EEP+  E+ E LR+  N+ S
Sbjct: 169 LIRDAIGPHVGIGVDFHGRVHRPMAKVLAKELEPFKLMFIEEPVLSENREALREIANHCS 228

Query: 243 LRIALGERIINKQQALYFMKEGLVDFLQADLYRIGGVTETKKVVGIAETFDVQMAFHNAQ 302
             IALGER+ ++      + +G VD +Q DL   GG+TE +K+  +AE +DV +A H   
Sbjct: 229 TPIALGERLYSRWDFKSVLSDGFVDIIQPDLSHAGGITECRKIAAMAEAYDVALAPHCPL 288

Query: 303 GPILNAVTLQFDAFIPNFLIQESFYDWFPSWKRELI-----YNGTPIDNGYAIIPERPGL 357
           GPI  A  LQ DA   N  IQE       +   +++           ++G+  IP+ PGL
Sbjct: 289 GPIALAACLQVDAVSYNAFIQEQSLGIHYNEANDILDYISNKEVFAYEDGFVSIPQGPGL 348

Query: 358 GVEVNEKMLDSLKVKGEEYFNPEEPVW 384
           G+EV+E  +     +G  + N   PVW
Sbjct: 349 GIEVDEAYVMERAKEGHRWRN---PVW 372


Lambda     K      H
   0.319    0.137    0.409 

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: 380
Number of extensions: 14
Number of successful extensions: 5
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: 393
Length of database: 382
Length adjustment: 30
Effective length of query: 363
Effective length of database: 352
Effective search space:   127776
Effective search space used:   127776
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: 50 (23.9 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