GapMind for catabolism of small carbon sources

 

Alignments for a candidate for eda in Sinorhizobium meliloti 1021

Align 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14) (characterized)
to candidate SMc03153 SMc03153 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase

Query= BRENDA::Q0K1X1
         (214 letters)



>FitnessBrowser__Smeli:SMc03153
          Length = 212

 Score =  207 bits (526), Expect = 2e-58
 Identities = 113/211 (53%), Positives = 130/211 (61%)

Query: 1   MQNQTSPLLQRLADVPVIPVLEFHSVDEALHVSEALVTGGLPLLEITLRTPVALEAIKAV 60
           M  +T  LL  L   PV+PVL       A+ ++ ALV GGL  +EITLRTP ALEAI+AV
Sbjct: 1   MSAKTDKLLSILKLQPVVPVLVIDDAGSAVPLARALVAGGLKAIEITLRTPAALEAIRAV 60

Query: 61  AAALPQACVGAGTVLNVEQLHAVRDAGAQFAVSPGLTPALAEGAQGAGISLLPGVATASE 120
           A  +  A  GAGT+LN  Q      AG+QF VSPG T  L + A    + LLPG ATASE
Sbjct: 61  ANEVEGAVAGAGTILNAAQFEEAVAAGSQFIVSPGTTQELIDVANDHEVPLLPGAATASE 120

Query: 121 AMAALEAGFTFLKFFPAQAAGGVPMLKSLGGPLPQLRFCPTGGIDAALAPTYLALPNVVC 180
            M   E G+  +KFFPA+ AGG   LKSL  PL    FCPTGGI  A A  YL LPNVVC
Sbjct: 121 VMGLREEGYDVMKFFPAEQAGGAAYLKSLSSPLAGTMFCPTGGISLANARDYLTLPNVVC 180

Query: 181 VGGSWVVPKDAVASGDWGRIRTLAEQARALR 211
           VGGSWV PKD V  GDW  I  LA +A AL+
Sbjct: 181 VGGSWVAPKDLVVRGDWAGITKLAAEAFALK 211


Lambda     K      H
   0.319    0.135    0.396 

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: 181
Number of extensions: 5
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: 214
Length of database: 212
Length adjustment: 22
Effective length of query: 192
Effective length of database: 190
Effective search space:    36480
Effective search space used:    36480
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: 45 (21.9 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