GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Bb in Desulfovibrio vulgaris Miyazaki F

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)

Query= uniprot:Q6MNM2
         (347 letters)



>FitnessBrowser__Miya:8501226
          Length = 399

 Score =  235 bits (599), Expect = 2e-66
 Identities = 116/253 (45%), Positives = 166/253 (65%), Gaps = 3/253 (1%)

Query: 4   IQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISID 63
           I+   + K+F     L  IDL I  GEFL L+GPSGCGK+T+LR ++G E   SG + I+
Sbjct: 8   IELRGVTKTFEDTVALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGEVRIN 67

Query: 64  GKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQI 123
           G+ +N + P+ R +  VFQ+YAL+PHMTV +N+ FGLK++ +AA E  +RV +   ++ +
Sbjct: 68  GQVVNRVPPEQRQVNTVFQNYALFPHMTVRDNVAFGLKMQGVAADETARRVLDALRMVHL 127

Query: 124 KHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNS 183
           ++  DRKP++LSGGQ+QRVA+ RA+     V+L DEP S LD  LR QM+LEIK L    
Sbjct: 128 ENFADRKPRQLSGGQQQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQLEIKHLQRQL 187

Query: 184 KSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFLE 243
             T ++VTHDQ EA  + DR+ V+ +G IEQIG P EIY  P N ++A F+G  ++N L 
Sbjct: 188 GITFVFVTHDQEEAFAMSDRVVVMNEGRIEQIGAPKEIYEEPANMYVARFVG--DINALP 245

Query: 244 GAV-LEKIPWPEA 255
           G +   ++ W  A
Sbjct: 246 GRIDAVRLDWSAA 258


Lambda     K      H
   0.318    0.136    0.383 

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: 313
Number of extensions: 12
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: 347
Length of database: 399
Length adjustment: 30
Effective length of query: 317
Effective length of database: 369
Effective search space:   116973
Effective search space used:   116973
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. 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