GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Bacteroides thetaiotaomicron VPI-5482

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)

Query= TCDB::Q8DQH7
         (236 letters)



>FitnessBrowser__Btheta:350819
          Length = 463

 Score =  115 bits (289), Expect = 1e-30
 Identities = 70/219 (31%), Positives = 124/219 (56%), Gaps = 4/219 (1%)

Query: 2   SVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIE 61
           S+++V ++S  +G   A+ DV+  V +GE V+++G +G GKTT+LR ++G    S G+I 
Sbjct: 8   SIIEVSHVSKFFGDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIR 67

Query: 62  FLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFS 121
             G+EI + P  K     ++ V +   +FP L V +N+  G  LKK  ++      K   
Sbjct: 68  ISGKEITQTPPHK---RPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAAL 124

Query: 122 RFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQD 181
           +   + + + +D  +LSGG+QQ +A+ RA+++ P++LLLDEP   L     +++   +++
Sbjct: 125 KMVGMTDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKE 184

Query: 182 IQKQ-GTTVLLIEQNANKALAISDRGYVLETGKIVLSGT 219
           + K  G T + +  +  +AL +SD   V+  GKI   GT
Sbjct: 185 MHKSLGITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGT 223


Lambda     K      H
   0.315    0.134    0.358 

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: 226
Number of extensions: 10
Number of successful extensions: 3
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: 236
Length of database: 463
Length adjustment: 28
Effective length of query: 208
Effective length of database: 435
Effective search space:    90480
Effective search space used:    90480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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