GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Paucidesulfovibrio gracilis DSM 16080

Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= SwissProt::P19566
         (369 letters)



>NCBI__GCF_900167125.1:WP_078717009.1
          Length = 370

 Score =  239 bits (611), Expect = 7e-68
 Identities = 136/328 (41%), Positives = 198/328 (60%), Gaps = 9/328 (2%)

Query: 4   VQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFIG 63
           ++L +V K +    V  D+ LDI  GEF+  +GPSGCGK+TLLR++AG E+ +SG++ + 
Sbjct: 8   IRLEHVAKEFDGETVLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEIILD 67

Query: 64  ETRMNDIPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVMNQRVNQVAEVLQL 123
              M D+PP  R V  VFQSYAL+PH+SV +N++FGL+++G  K  + +RV +   ++ L
Sbjct: 68  GRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMVGL 127

Query: 124 AHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLHKRL 183
           A    R+P +LSGGQ+QRVAI R +V  P V LLDEPLS LD  LRVQMR E+ +L + +
Sbjct: 128 AGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRREM 187

Query: 184 GRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMNFLP 243
           G T I+VTHDQ EA +++D++VV++ G VAQVG P+E+Y  P + FVA F+G   +    
Sbjct: 188 GITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVGETNVFEGV 247

Query: 244 VKVTATAIEQVQVELPNRQQIWLPVESRGVQVGANMSLGIRPEHLL-----PSDIADVTL 298
              +   I Q  VE    +        RG Q G  + + +RPE LL     P D   + L
Sbjct: 248 AGQSDGGILQALVEGRTCEL----SSHRGFQPGDRIRVLLRPEDLLVEREEPEDDDKLWL 303

Query: 299 EGEVQVVEQLGHETQIHIQIPAIRQNLV 326
            G +      G    + +Q+ +  + LV
Sbjct: 304 PGRIMETVYKGSTWDMVVQLDSGHEILV 331


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: 353
Number of extensions: 17
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: 369
Length of database: 370
Length adjustment: 30
Effective length of query: 339
Effective length of database: 340
Effective search space:   115260
Effective search space used:   115260
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 Apr 09 2024. 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