GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_17605 in Bacteroides thetaiotaomicron VPI-5482

Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate 353166 BT3640 lipoprotein releasing system ATP-binding protein (NCBI ptt file)

Query= uniprot:A0A1N7U8S3
         (276 letters)



>lcl|FitnessBrowser__Btheta:353166 BT3640 lipoprotein releasing
           system ATP-binding protein (NCBI ptt file)
          Length = 218

 Score =  134 bits (338), Expect = 1e-36
 Identities = 79/228 (34%), Positives = 135/228 (59%), Gaps = 14/228 (6%)

Query: 27  LQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLD 86
           +++EGI K +G  +VLKG+ L   +G+++S++G SG+GK+T+L+ +  L++PDAG + +D
Sbjct: 2   IKLEGITKSFGSLQVLKGIDLEINKGEIVSIVGPSGAGKTTLLQIMGTLDEPDAGTVAID 61

Query: 87  GISIEMRQGRAGTRAPHQDQLQNLRTR-LAMVFQHFNLWSHMTVLENITMAPRRVLDVSA 145
           G  +   +         + +L   R + +  VFQ   L    T LEN+ M P  +  VS+
Sbjct: 62  GTVVSRMK---------EKELSAFRNKNIGFVFQFHQLLPEFTALENV-MIPAFIAGVSS 111

Query: 146 AEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDP 205
            EA +RA   L  +GL  R A   P  LSGG++QRVA+ARAL   P +IL DEP+ +LD 
Sbjct: 112 KEANERAMEILAFMGLTDR-ASHKPNELSGGEKQRVAVARALINHPAVILADEPSGSLDT 170

Query: 206 ELVGEVLKVIQTLAEE-GRTMLMVTHEMGFARQVSSQVLFLHQGRVEE 252
               ++ ++   L +  G+T ++VTH+ G A+ ++ + + +  G +++
Sbjct: 171 HNKEDLHQLFFDLRDRLGQTFVIVTHDEGLAK-ITDRTVHMVDGTIKK 217


Lambda     K      H
   0.319    0.133    0.372 

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: 144
Number of extensions: 7
Number of successful extensions: 4
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: 276
Length of database: 218
Length adjustment: 24
Effective length of query: 252
Effective length of database: 194
Effective search space:    48888
Effective search space used:    48888
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: 46 (22.3 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