GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gluC in Desulfovibrio vulgaris Miyazaki F

Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate 8500595 DvMF_1343 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= TCDB::P48244
         (228 letters)



>lcl|FitnessBrowser__Miya:8500595 DvMF_1343 polar amino acid ABC
           transporter, inner membrane subunit (RefSeq)
          Length = 337

 Score =  105 bits (261), Expect = 1e-27
 Identities = 70/221 (31%), Positives = 115/221 (52%), Gaps = 22/221 (9%)

Query: 12  LLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTLVVLFC 71
           LL   W+T+++++ + IG ++ G +    R+S   +LR  +  YI  +R +PL + +   
Sbjct: 127 LLEGLWITLEVSVLAIIGGIVIGVVTGLCRISINPMLRWGAITYIEIIRGSPLLVQIFLW 186

Query: 72  SF-------GLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINTVH 124
            F        L +++GL   G  S  +         V+   L+T  +VAE +R+GI +VH
Sbjct: 187 YFVVGTLINALLEHVGL---GGISPLWY-------GVMALALFTGAYVAEIVRAGIQSVH 236

Query: 125 FGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEASLLM 184
            GQ EAARSLG+ +    R +I PQA R  + PL    I+L K++++  VI + E   L 
Sbjct: 237 RGQMEAARSLGMNYAQAMRKVILPQAFRRIMPPLAGQFISLIKDSSLLGVIAIRE---LT 293

Query: 185 KATIENHANML--FVVFAIFAVGFMILTLPMGLGLGKLSER 223
           KAT E     L  F ++ + AV +++LT  + L +  L  R
Sbjct: 294 KATREVVTTSLQPFELWIVCAVLYLVLTFTLSLFVQYLERR 334


Lambda     K      H
   0.327    0.139    0.397 

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: 169
Number of extensions: 4
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: 228
Length of database: 337
Length adjustment: 25
Effective length of query: 203
Effective length of database: 312
Effective search space:    63336
Effective search space used:    63336
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 (21.7 bits)
S2: 47 (22.7 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