Aligments for a candidate for H281DRAFT_01113 in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments for a candidate for H281DRAFT_01113 in Burkholderia phytofirmans PsJN

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate BPHYT_RS25790 BPHYT_RS25790 sugar ABC transporter ATP-binding protein

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>FitnessBrowser__BFirm:BPHYT_RS25790
          Length = 500

 Score =  904 bits (2335), Expect = 0.0
 Identities = 465/500 (93%), Positives = 486/500 (97%)

Query: 16  LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75
           ++VVGVHKRFTGVHALRGVSLSF+RGQIYHLLGENGCGKSTLIKIISGAQPPDEG+LVIE
Sbjct: 1   MQVVGVHKRFTGVHALRGVSLSFERGQIYHLLGENGCGKSTLIKIISGAQPPDEGELVIE 60

Query: 76  GVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAA 135
           GV HARLSALE+LAAGIETVYQDLSLLPNM+VAENVALTSELATH+G+LARTFDRR LA 
Sbjct: 61  GVRHARLSALESLAAGIETVYQDLSLLPNMNVAENVALTSELATHQGKLARTFDRRELAR 120

Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195
           TAARALEAVGLPGN+EFQ+TLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV
Sbjct: 121 TAARALEAVGLPGNAEFQATLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 180

Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255
           DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIA+FTKAQISELM
Sbjct: 181 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAQFTKAQISELM 240

Query: 256 TGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELAR 315
           TGRHLSNERYRE AH  +IVL+VRG+TRAGQFSDVSF LHGGEILG+TGLLDSGRNELAR
Sbjct: 241 TGRHLSNERYREGAHEPNIVLEVRGYTRAGQFSDVSFGLHGGEILGITGLLDSGRNELAR 300

Query: 316 ALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMI 375
           ALAGVAPAQSG V LDG+ I+LRTPSDAK HRIGYVPEDRLNEGLFLDKPIRDNVITAMI
Sbjct: 301 ALAGVAPAQSGQVRLDGKSISLRTPSDAKNHRIGYVPEDRLNEGLFLDKPIRDNVITAMI 360

Query: 376 SSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRV 435
           SSLRDRFGQIDR RAQALAEQTVK+LQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRV
Sbjct: 361 SSLRDRFGQIDRVRAQALAEQTVKDLQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRV 420

Query: 436 LILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAE 495
           LILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKG V++E
Sbjct: 421 LILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGRVASE 480

Query: 496 YRADELSEADLYHALLSEAA 515
           Y+AD LSEADLYHALLSEAA
Sbjct: 481 YQADTLSEADLYHALLSEAA 500


Lambda     K      H
   0.319    0.135    0.376 

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: 911
Number of extensions: 25
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: 515
Length of database: 500
Length adjustment: 34
Effective length of query: 481
Effective length of database: 466
Effective search space:   224146
Effective search space used:   224146
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 (21.7 bits)
S2: 52 (24.6 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources