GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SM_b21106 in Bacteroides thetaiotaomicron VPI-5482

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)

Query= reanno::Smeli:SM_b21106
         (365 letters)



>lcl|FitnessBrowser__Btheta:350819 BT1291 spermidine/putrescine
           transport ATP-binding protein (NCBI ptt file)
          Length = 463

 Score =  218 bits (554), Expect = 3e-61
 Identities = 113/282 (40%), Positives = 165/282 (58%), Gaps = 5/282 (1%)

Query: 4   VTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63
           + +  + K +G    +  + L VK  EF+ ++GPSGCGK+T LR+IAG +  S G I I 
Sbjct: 10  IEVSHVSKFFGDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIRIS 69

Query: 64  GRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDL 123
           G+++   PP  R ++ VFQ YAL+PH+ V +N+ F LK+   P + I  +V  A  ++ +
Sbjct: 70  GKEITQTPPHKRPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAALKMVGM 129

Query: 124 AHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARM 183
                R    LSGGQ+QRVA+ RAIV +P+V L DEPL+ LD K+R  ++ E+K++H  +
Sbjct: 130 TDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHKSL 189

Query: 184 QATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNMEE 243
             T +YVTHDQ EA+TLSD IV+M +G I+Q+GTP D++  P   FVA FIG    N+  
Sbjct: 190 GITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIGE--SNILN 247

Query: 244 AVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVY 285
             +   KL    G              E   V   +RP+D+Y
Sbjct: 248 GTMIHDKLVRFCGTEFECVDEG---FGENTPVDVVIRPEDLY 286


Lambda     K      H
   0.320    0.137    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: 387
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: 365
Length of database: 463
Length adjustment: 31
Effective length of query: 334
Effective length of database: 432
Effective search space:   144288
Effective search space used:   144288
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, 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