GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Desulfovibrio vulgaris Hildenborough

Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein

Query= SwissProt::Q9YGA6
         (372 letters)



>MicrobesOnline__882:208681
          Length = 349

 Score =  290 bits (743), Expect = 3e-83
 Identities = 168/368 (45%), Positives = 226/368 (61%), Gaps = 25/368 (6%)

Query: 1   MAGVRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQI 60
           M+ + L  V + +G+V AV ++S EV+ G+ ++LLGPSGCGK+TTLR+IAGLE  + G+I
Sbjct: 1   MSTIVLDKVSRHWGDVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSGRI 60

Query: 61  YIGDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRV 120
            IG + V +      +PP  R +AMVFQSYAL+PH+TV DNI F L +RKVP  E  +R+
Sbjct: 61  LIGGRDVTN------LPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKRL 114

Query: 121 REVAELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRA 180
               E+LGL +LL RKP ELSGGQ+QRVALGRA+V +  V LMDEPLSNLDAKLR  MR 
Sbjct: 115 DRAVEILGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRR 174

Query: 181 ELKKLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFI 240
           E++ LQ+ LG+T +YVTHDQ EAM+M DRI +M  G + Q  +P E+Y +PA  F   FI
Sbjct: 175 EIRALQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFI 234

Query: 241 GSPPMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGELGYVGREVIFGIRPEDLYDAMFA 300
           G+PPMN +     +DG    G    ++            + G + + GIRPE        
Sbjct: 235 GTPPMNLVRLQGNDDGIRVAGSRSGRV----------TCHAGADCMLGIRPE-------- 276

Query: 301 QVRVPGENLVRAVVEIVENLGSERIVHLRVGGVTFVGSFRSESRVREGVEVDVVFDMKKI 360
            +R+  +   RAVVE VE LGS  ++  RVG           +    G E+ +    + +
Sbjct: 277 HIRIVDDGW-RAVVESVEYLGSNSVLSCRVGSEELSVVVHGVTDTVVGAEIYLHCPEEHV 335

Query: 361 HIFDKTTG 368
           HIFD  TG
Sbjct: 336 HIFDAATG 343


Lambda     K      H
   0.323    0.142    0.406 

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: 369
Number of extensions: 14
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: 372
Length of database: 349
Length adjustment: 29
Effective length of query: 343
Effective length of database: 320
Effective search space:   109760
Effective search space used:   109760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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