GapMind for catabolism of small carbon sources

 

Aligments for a candidate for araV in Desulfovibrio vulgaris Miyazaki F

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)

Query= TCDB::Q97UF2
         (371 letters)



>lcl|FitnessBrowser__Miya:8501226 DvMF_1960 putrescine/spermidine
           ABC transporter ATPase protein (RefSeq)
          Length = 399

 Score =  198 bits (504), Expect = 2e-55
 Identities = 103/250 (41%), Positives = 161/250 (64%), Gaps = 9/250 (3%)

Query: 4   IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63
           I +  ++K F+    +  A+D++ +TI +G    +LGPSG GKTT LRL++G E+PTSG 
Sbjct: 8   IELRGVTKTFE----DTVALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGE 63

Query: 64  IYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKV 123
           +  + + V+      + PE+R +  VFQN+AL+P+MTV DN+AF LK+  V  D+   +V
Sbjct: 64  VRINGQVVNR-----VPPEQRQVNTVFQNYALFPHMTVRDNVAFGLKMQGVAADETARRV 118

Query: 124 KEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARA 183
            +    + L    +R P++LSGGQ QR AIARA++ +P VLLLDEPFS LD ++R+  + 
Sbjct: 119 LDALRMVHLENFADRKPRQLSGGQQQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQL 178

Query: 184 LVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLT 243
            ++ +QR+  +T + V+HD  + FA++++  V+  G+  QIG P EIYE PA   +AR  
Sbjct: 179 EIKHLQRQLGITFVFVTHDQEEAFAMSDRVVVMNEGRIEQIGAPKEIYEEPANMYVARFV 238

Query: 244 GEINLIQAKI 253
           G+IN +  +I
Sbjct: 239 GDINALPGRI 248


Lambda     K      H
   0.317    0.136    0.374 

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: 308
Number of extensions: 14
Number of successful extensions: 2
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: 371
Length of database: 399
Length adjustment: 30
Effective length of query: 341
Effective length of database: 369
Effective search space:   125829
Effective search space used:   125829
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: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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