GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS17020 in Desulfovibrio vulgaris Miyazaki F

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)

Query= uniprot:D8IPI1
         (406 letters)



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

 Score =  233 bits (594), Expect = 7e-66
 Identities = 118/228 (51%), Positives = 159/228 (69%), Gaps = 2/228 (0%)

Query: 20  LHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNVA 79
           L  +DL I +GEF+ LLGPSGCGK+T+LR+++G E  + G +RI G VVN +P  +R V 
Sbjct: 23  LDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGEVRINGQVVNRVPPEQRQVN 82

Query: 80  MVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGGQ 139
            VFQNYAL+PHM+V DN+AFGL+     A E  RRV +   +++LE   +RKPR +SGGQ
Sbjct: 83  TVFQNYALFPHMTVRDNVAFGLKMQGVAADETARRVLDALRMVHLENFADRKPRQLSGGQ 142

Query: 140 QQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEAM 199
           QQR AIARA+I  P V L DEP S LD KLR Q++ +IK L ++L  T V+VTHDQ EA 
Sbjct: 143 QQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQLEIKHLQRQLGITFVFVTHDQEEAF 202

Query: 200 TLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTV 247
            ++DRV++M +GRI Q G+P E+Y  P N++ A F+G   +N L G +
Sbjct: 203 AMSDRVVVMNEGRIEQIGAPKEIYEEPANMYVARFVGD--INALPGRI 248


Lambda     K      H
   0.321    0.137    0.403 

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: 384
Number of extensions: 14
Number of successful extensions: 1
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: 406
Length of database: 399
Length adjustment: 31
Effective length of query: 375
Effective length of database: 368
Effective search space:   138000
Effective search space used:   138000
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: 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