GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Desulfovibrio vulgaris Miyazaki F

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate 8500849 DvMF_1587 ABC transporter related (RefSeq)

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__Miya:8500849
          Length = 366

 Score =  202 bits (514), Expect = 1e-56
 Identities = 130/322 (40%), Positives = 181/322 (56%), Gaps = 22/322 (6%)

Query: 1   MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60
           MAD+ L G+ KAYG   VL  ++L +  GE    +GPSGCGK+ LLR+IAG E    GT+
Sbjct: 1   MADITLAGIGKAYGAHAVLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAGTI 60

Query: 61  EIDGTVVND------VPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAV 114
            I G  V+D      VPP  R + +VFQ YA++PHM+V +N+ + LK+A    AE    V
Sbjct: 61  SIGGEPVSDAVTGDCVPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERTRQV 120

Query: 115 EAAAEKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRL 174
               E + L    +R+P  LSGGQ+QRVA+ R++V  P + L DEPL NLDA LR   R 
Sbjct: 121 LETVEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREEMRF 180

Query: 175 EIAQLKEAMPESTMVYVTHDQVEAMTLATRIVVL-AGGGIAQVGSPLELYEKPENEFVAQ 233
           EI +L+  +   T++YVTHDQ  A+ ++ R+ ++   G I QVG+P E++E+P +EFV +
Sbjct: 181 EIKELQRTL-GITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFVFR 239

Query: 234 FIGSPKMNLLPGKIIGTGAQTTVEMTDGGRAVSDY--PSDDSLMGAAVNVGVRPEDMVEA 291
           F+G    N LP +  G        +  GG     +  P  D+    A   G RP D V  
Sbjct: 240 FMG--VANFLPARRRGMAM-----LAAGGEQPVPWGLPDGDAEHWMA---GFRPSD-VRL 288

Query: 292 APGGDYVFEGKVAITEALGEVT 313
           A  GD +  G V     LG +T
Sbjct: 289 ARQGDGL-RGTVRRASFLGAMT 309


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: 370
Number of extensions: 27
Number of successful extensions: 4
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: 366
Length adjustment: 30
Effective length of query: 343
Effective length of database: 336
Effective search space:   115248
Effective search space used:   115248
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 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