GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Paucidesulfovibrio gracilis DSM 16080

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_900167125.1:WP_078717009.1
          Length = 370

 Score =  215 bits (547), Expect = 2e-60
 Identities = 121/286 (42%), Positives = 176/286 (61%), Gaps = 4/286 (1%)

Query: 4   LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63
           ++L  V K +    VL ++ LDI+ GE +  +GPSGCGK+TLLR++AG E  + G + +D
Sbjct: 8   IRLEHVAKEFDGETVLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEIILD 67

Query: 64  GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQL 123
           G  + DVPP  R +  VFQSYAL+PHM+V +N++F L+++   + EI   V  A   + L
Sbjct: 68  GRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMVGL 127

Query: 124 GQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAM 183
                R P +LSGGQ+QRVAI R++V  P V L DEPLS LD  LRV  R E+ QL+  M
Sbjct: 128 AGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRREM 187

Query: 184 PESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLL 243
              T ++VTHDQ EA +++ R+VV+  G +AQVG+P+E+YE+P N FVA+F+G  + N+ 
Sbjct: 188 -GITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVG--ETNVF 244

Query: 244 PGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMV 289
            G + G      ++    GR            G  + V +RPED++
Sbjct: 245 EG-VAGQSDGGILQALVEGRTCELSSHRGFQPGDRIRVLLRPEDLL 289


Lambda     K      H
   0.316    0.135    0.379 

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: 365
Number of extensions: 20
Number of successful extensions: 2
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: 373
Length of database: 370
Length adjustment: 30
Effective length of query: 343
Effective length of database: 340
Effective search space:   116620
Effective search space used:   116620
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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