GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Phaeobacter inhibens BS107

Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate GFF776 PGA1_c07900 alpha-glucoside transport ATP-binding protein AglK

Query= BRENDA::P68187
         (371 letters)



>FitnessBrowser__Phaeo:GFF776
          Length = 363

 Score =  331 bits (848), Expect = 2e-95
 Identities = 180/357 (50%), Positives = 241/357 (67%), Gaps = 5/357 (1%)

Query: 1   MASVQLQNVTKAWGE-VVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGD 59
           MA+++L NV K +G  V V +DINLDI +GE +VFVGPSGCGKSTLLRMIAGLE I+ G 
Sbjct: 1   MANLKLTNVAKTYGGGVEVLRDINLDIKQGELIVFVGPSGCGKSTLLRMIAGLERISGGT 60

Query: 60  LFIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAE 119
           L I    MND PPA+RG+ MVFQSYALYPH++V +NM+F LK+A   K+ I+  +++ A+
Sbjct: 61  LEIDNAVMNDIPPAQRGIAMVFQSYALYPHMTVRDNMAFALKIAKKSKDEIDAAIDRAAK 120

Query: 120 VLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRL 179
           +LQL   LDR PKALSGGQRQRVAIGR++V +P V+L DEPLSNLDAALRV  RIEI++L
Sbjct: 121 ILQLEPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRIEIAQL 180

Query: 180 HKRL-GRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPK 238
            + +   TMIYVTHDQVEAMTLA +IVVL    +AQVG PL+LY  P + FVA FIGSP 
Sbjct: 181 KEAMPDSTMIYVTHDQVEAMTLASRIVVLADKGIAQVGTPLDLYQRPENEFVAQFIGSPA 240

Query: 239 MNFLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIADV 298
           MN +P  V AT     +  + + + ++V   + + D   G  +++G+RPE L+       
Sbjct: 241 MNLIPGTVVATG---PRTTVRLTSGEEVVAEIPTTDADQGLAVNVGVRPEDLVEEGTGGA 297

Query: 299 ILEGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLF 355
           +++  V +VE LG  T ++I     +  L+ +   +     G++  +   P R HLF
Sbjct: 298 LIDSRVDIVEALGEVTVLYIAAGEGKDPLIAKLPGIHKGLRGSSVRLYADPARLHLF 354


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: 374
Number of extensions: 13
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: 371
Length of database: 363
Length adjustment: 30
Effective length of query: 341
Effective length of database: 333
Effective search space:   113553
Effective search space used:   113553
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