GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Synechococcus elongatus PCC 7942

Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1

Query= BRENDA::P68187
         (371 letters)



>FitnessBrowser__SynE:Synpcc7942_1680
          Length = 338

 Score =  215 bits (547), Expect = 2e-60
 Identities = 112/240 (46%), Positives = 155/240 (64%), Gaps = 2/240 (0%)

Query: 4   VQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFIG 63
           +Q+  V+K +G     KD++L +  G  V  +GPSG GKSTLLR+IAGLE   SG +F+ 
Sbjct: 3   IQVSQVSKQFGSFQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIFLT 62

Query: 64  EKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEVLQL 123
            +   +    +R +G VFQ YAL+ HL+V +N++FGL+L    KE +  RV ++ E++QL
Sbjct: 63  GRDATNESVRDRQIGFVFQHYALFKHLTVRKNIAFGLELRKHTKEKVRARVEELLELVQL 122

Query: 124 AHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLHKRL 183
             L DR P  LSGGQRQRVA+ R L  +P V LLDEP   LDA +R  +R  + +LH  +
Sbjct: 123 TGLGDRYPSQLSGGQRQRVALARALAVQPQVLLLDEPFGALDAKVRKDLRSWLRKLHDEV 182

Query: 184 GRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMNFLP 243
             T ++VTHDQ EAM +AD+IVV++ G+V Q+G P E+Y  PA  FV  FIG   +N LP
Sbjct: 183 HVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDNPATPFVMSFIG--PVNVLP 240


Lambda     K      H
   0.320    0.137    0.393 

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: 304
Number of extensions: 13
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: 371
Length of database: 338
Length adjustment: 29
Effective length of query: 342
Effective length of database: 309
Effective search space:   105678
Effective search space used:   105678
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: 49 (23.5 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