GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Corynebacterium deserti GIMN1.010

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_053544618.1 CDES_RS05420 amino acid permease

Query= TCDB::Q2VQZ4
         (536 letters)



>NCBI__GCF_001277995.1:WP_053544618.1
          Length = 468

 Score =  217 bits (552), Expect = 9e-61
 Identities = 133/410 (32%), Positives = 206/410 (50%), Gaps = 14/410 (3%)

Query: 37  LKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALAEMAVLY 96
           L+ RH+  IA+G AIG GLF GS GA+Q  GP+ LL+ YL+ G ++     AL EM+V +
Sbjct: 14  LRARHIHFIALGSAIGTGLFYGSAGAIQAAGPSVLLV-YLLGGAVVYFMLRALGEMSVHH 72

Query: 97  PVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINMAVWVSV 156
           PV G+F  Y    +    G+  GW +A   L V   +L A  I + FW  D    VWV+ 
Sbjct: 73  PVRGSFAVYTRAHLGGWAGYITGWMFAFEMLIVCLADLTAIGIYMNFWFPDTPQWVWVAA 132

Query: 157 FLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYIG--VKYWR 214
            L+++ G  +  VR +GE+E V +I+K+ A +  I+ G  I   G+G    +      W 
Sbjct: 133 TLLIVGGANLASVRWFGELEVVFTIVKVTAVIAMIVGGAAILAFGLGSNAEVAGISNLWE 192

Query: 215 DPGAF-TSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIAIFYIL 273
             G F    +G  A F++  F+FGGTE++G+A +E+  P KSIP A   V  RI +FY+ 
Sbjct: 193 HGGFFPNGIEGMIAAFILVLFAFGGTEIIGVAGSEAEEPEKSIPKAVNTVPVRILLFYVG 252

Query: 274 NLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLSVANSC 333
            + ++  + P   P + G      + SPFV      G+     ++N V+  A LS  N+ 
Sbjct: 253 AILVILALNPW--PSITG------EESPFVQIFDTLGVNWAAGLLNLVVITAALSAINAD 304

Query: 334 TFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGMEIFGWLL 393
            FG+ R +  +A+ N+AP     I   G P+   I+ I   ++  I  A     +F  + 
Sbjct: 305 LFGAGRVLTGLAKENLAPKAMGKIAKNGVPIMTTIIMIIVLIVGVILNAVLPERVFEIVA 364

Query: 394 ALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFGVAGSYLGL 443
           +L     ++VW  I LA +  R  M A+ +    + +  PF   G Y  +
Sbjct: 365 SLATFATVYVWLMILLAQVGSRRRMSAEEVE--TLKFPVPFYPFGQYFAI 412


Lambda     K      H
   0.327    0.142    0.442 

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: 589
Number of extensions: 35
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 536
Length of database: 468
Length adjustment: 34
Effective length of query: 502
Effective length of database: 434
Effective search space:   217868
Effective search space used:   217868
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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