GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Synechococcus elongatus PCC 7942

Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase

Query= SwissProt::P19566
         (369 letters)



>FitnessBrowser__SynE:Synpcc7942_0960
          Length = 417

 Score =  283 bits (725), Expect = 5e-81
 Identities = 173/380 (45%), Positives = 229/380 (60%), Gaps = 41/380 (10%)

Query: 14  GDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFIGETRMNDIPPA 73
           G+VVV   INL+I DGEF+V VGPSGCGKSTLLR++AGLET + G + +G+ R++ +P  
Sbjct: 45  GEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDRLPAK 104

Query: 74  ERGVGMVFQSYALYPHLSVAENMSFGLKLAGAK------------------------KEV 109
            R + MVFQSYALYPHLSV +N++FGL+  G +                        +  
Sbjct: 105 ARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPEQEAR 164

Query: 110 MNQRVNQVAEVLQLAHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALR 169
           + +RV +VA +LQL  LL+R+PK LSGGQ+QRVA+GR +   P+VFL+DEPLSNLDA LR
Sbjct: 165 IKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRAIARNPQVFLMDEPLSNLDAKLR 224

Query: 170 VQMRIEISRLHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRF 229
            + R +I  L ++LG T +YVTHDQ EAMT+ D+I VL+ G + QV  PLE+Y  PA+RF
Sbjct: 225 AETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDRPANRF 284

Query: 230 VAGFIGSPKMNFLPVKVTA---TAIEQVQVELPNRQQIWLPVESRGVQVGANMSLGIRPE 286
           VA FIGSP MN +PV V A      E  +  LP   + W PV    +  G  + LGIRPE
Sbjct: 285 VAQFIGSPPMNLIPVTVRAPLQLTTENFRCTLP---EAWEPV--LRLYDGQTVELGIRPE 339

Query: 287 HLLPSDIADVTLEGEVQVVEQLGHETQIHIQIP----AIRQNLVYRQNDVVLVEEGATFA 342
           HL     A   L   V  VE LG +T I  ++     A++  L  +Q      + G    
Sbjct: 340 HLEVGAAASKNLLITVTGVEALGSDTFIAGELKESGIAVQARLAPQQ----CWQMGDRLW 395

Query: 343 IGLPPERCHLF-REDGSACR 361
           +   P++ HLF  E G A R
Sbjct: 396 LTFKPDQIHLFDLETGKAIR 415


Lambda     K      H
   0.321    0.138    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: 401
Number of extensions: 18
Number of successful extensions: 3
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: 369
Length of database: 417
Length adjustment: 31
Effective length of query: 338
Effective length of database: 386
Effective search space:   130468
Effective search space used:   130468
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: 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