GapMind for catabolism of small carbon sources

 

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

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)

Query= TCDB::P73650
         (240 letters)



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

 Score =  105 bits (263), Expect = 1e-27
 Identities = 66/218 (30%), Positives = 118/218 (54%), Gaps = 6/218 (2%)

Query: 14  YVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLG 73
           +  D   L  +  ++  GE VT++GP+G GK+TL + I G  T S+GEI   G+ IT   
Sbjct: 18  FFGDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIRISGKEITQTP 77

Query: 74  SDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFPK--LAQRRN 131
                +R +  V Q   +F  L V +N+  G  L + P QT+  ++        +     
Sbjct: 78  PH---KRPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAALKMVGMTDYEY 134

Query: 132 QRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAIN-ATGKAII 190
           +   +LSGG++Q +A+ RA++ +P++LLLDEP AAL   + KD+  ++K ++ + G   +
Sbjct: 135 RDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHKSLGITFV 194

Query: 191 LVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPL 228
            V  + ++AL ++D   V+  G+ +  G+   + N+P+
Sbjct: 195 YVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPI 232


Lambda     K      H
   0.320    0.139    0.393 

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: 216
Number of extensions: 11
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: 240
Length of database: 463
Length adjustment: 28
Effective length of query: 212
Effective length of database: 435
Effective search space:    92220
Effective search space used:    92220
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: 49 (23.5 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