GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artM in Desulfovibrio vulgaris Hildenborough

Align L-Arginine ABC transporter, permease component 1 (characterized)
to candidate 206098 DVU0674 ABC transporter, permease protein, His/Glu/Gln/Arg/opine family

Query= reanno::pseudo5_N2C3_1:AO356_18710
         (232 letters)



>lcl|MicrobesOnline__882:206098 DVU0674 ABC transporter, permease
           protein, His/Glu/Gln/Arg/opine family
          Length = 271

 Score =  123 bits (308), Expect = 4e-33
 Identities = 73/210 (34%), Positives = 117/210 (55%), Gaps = 12/210 (5%)

Query: 14  LYFSGLLTTLKLLALSLFFGLLAALPLGLMRVSKQPIVNMTAWLYTYVIRGTPMLVQLFL 73
           L   GL  TL++ A SL   LL A     +R+S      + A LY   +R TP+LVQLF+
Sbjct: 68  LLLQGLGVTLQVAAGSLVLALLLAAVAVALRLSCLRTGRLVARLYVESVRNTPLLVQLFV 127

Query: 74  IYYGLAQ-FAIVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIEAAK 132
            Y+ +A  F + R +            A +A  +   AY AEI+   + A P G+ EA++
Sbjct: 128 TYFAIAPVFGLGRMA-----------SAVMALGVFEGAYMAEILRAGIAAVPQGQWEASR 176

Query: 133 AMGMSRYKLYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQYY 192
           ++GM     Y +++LP ALRRALP  + + + +++ +SLAS + + ++T  A+T+ A+ +
Sbjct: 177 SLGMDEPGTYVQVILPQALRRALPPLTGQAVSLVKDSSLASAIAIHELTMQAQTIIAETF 236

Query: 193 LPFEAYITAGAFYLCLTFILVRLFKLAERR 222
           L FE ++   A YLC+T  L  + +L ERR
Sbjct: 237 LTFEVWLLTAAIYLCVTLSLSAVARLLERR 266


Lambda     K      H
   0.330    0.140    0.425 

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: 140
Number of extensions: 2
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: 232
Length of database: 271
Length adjustment: 24
Effective length of query: 208
Effective length of database: 247
Effective search space:    51376
Effective search space used:    51376
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 46 (22.3 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, the preprint on GapMind for carbon sources, 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