GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate 8500849 DvMF_1587 ABC transporter related (RefSeq)

Query= reanno::Smeli:SMc03065
         (362 letters)



>FitnessBrowser__Miya:8500849
          Length = 366

 Score =  218 bits (556), Expect = 2e-61
 Identities = 136/325 (41%), Positives = 189/325 (58%), Gaps = 19/325 (5%)

Query: 1   MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60
           M  + L  I K+YGA  V+ G+ L +  GE    +GPSGCGK+ LLR+IAG E    G +
Sbjct: 1   MADITLAGIGKAYGAHAVLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAGTI 60

Query: 61  FIDGERVND------VPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRV 114
            I GE V+D      VPP  R + +VFQ YA++PHM+V DN+ + +++A     E  R+V
Sbjct: 61  SIGGEPVSDAVTGDCVPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERTRQV 120

Query: 115 RGAADMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRI 174
               +M+ LT   +R+P  LSGGQ+QRVA+ RA+   P + L DEPL NLDA LR   R 
Sbjct: 121 LETVEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREEMRF 180

Query: 175 EIAKLSERMSDTTMIYVTHDQVEAMTLADRIVVLS-AGHIEQVGAPLELYERPANLFVAR 233
           EI +L +R    T++YVTHDQ  A+ ++DR+ ++  AG I QVG P E++ERPA+ FV R
Sbjct: 181 EIKEL-QRTLGITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFVFR 239

Query: 234 FIGSPAMNVIPATITATGQQTAVSLAGGKS-VTLDVPTNASENGKTASFGVRPEDLRVTE 292
           F+G    N +P    A  +  A+  AGG+  V   +P   +E+      G RP D+R+  
Sbjct: 240 FMG--VANFLP----ARRRGMAMLAAGGEQPVPWGLPDGDAEHWMA---GFRPSDVRLAR 290

Query: 293 ADDFLFEGTVSIVEALGEVTLLYIE 317
             D L  GTV     LG +T   IE
Sbjct: 291 QGDGL-RGTVRRASFLGAMTDYLIE 314


Lambda     K      H
   0.320    0.137    0.387 

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: 326
Number of extensions: 15
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: 362
Length of database: 366
Length adjustment: 29
Effective length of query: 333
Effective length of database: 337
Effective search space:   112221
Effective search space used:   112221
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