GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Desulfovibrio vulgaris Miyazaki F

Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 8499890 DvMF_0655 ABC transporter related (RefSeq)

Query= SwissProt::Q9YGA6
         (372 letters)



>FitnessBrowser__Miya:8499890
          Length = 350

 Score =  292 bits (747), Expect = 1e-83
 Identities = 173/369 (46%), Positives = 230/369 (62%), Gaps = 25/369 (6%)

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

Query: 61  YIGDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRV 120
            IG++ V        +PP  R +AMVFQSYAL+PH+TV +NI F L +RKVP  E ++R+
Sbjct: 61  MIGERDVTH------LPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKRL 114

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

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

Query: 241 GSPPMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGELGYVGREVIFGIRPEDLYDAMFA 300
           G+PPMN L  +    G V     R         V+    YV      GIRPE        
Sbjct: 235 GTPPMN-LVRLDDARGSVCVAGSR----SGTVSVVDSADYV-----LGIRPE-------- 276

Query: 301 QVRVPGENLVRAVVEIVENLGSERIVHLRVGGVTFVGSFRSESRVREGVEVDVVFDMKKI 360
            +R+  E   RAVVE VE LGS  ++  RVGG            +  G E+ +    + I
Sbjct: 277 HIRIVPEGW-RAVVESVEYLGSGSVLGCRVGGEELSVVVDGVPTIAVGAEIYLHCPDEHI 335

Query: 361 HIFDKTTGK 369
           HIFD  TG+
Sbjct: 336 HIFDAKTGE 344


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: 372
Number of extensions: 19
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: 350
Length adjustment: 29
Effective length of query: 343
Effective length of database: 321
Effective search space:   110103
Effective search space used:   110103
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