Alignments for a candidate for BPHYT_RS16930 in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS16930 in Paraburkholderia bryophila 376MFSha3.1

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate H281DRAFT_01057 H281DRAFT_01057 monosaccharide ABC transporter ATP-binding protein, CUT2 family (TC 3.A.1.2.-)

Query= uniprot:A0A165ZSX8
         (514 letters)



>FitnessBrowser__Burk376:H281DRAFT_01057
          Length = 517

 Score =  377 bits (967), Expect = e-109
 Identities = 204/494 (41%), Positives = 307/494 (62%), Gaps = 5/494 (1%)

Query: 13  GGSLRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDL 72
           G  L    I K FPGV++L  +S     G++HAL+GENGAGKSTL KI+ G Y P SG++
Sbjct: 10  GDLLEVIRITKEFPGVKSLDQVSLGVRAGEIHALVGENGAGKSTLTKIMAGVYAPDSGEI 69

Query: 73  QIGEQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLP-ARFGLVNRGVLRQQ 131
           +   Q + +K  AD+   G+ VIHQEL L P+ TVAEN+F G  P  R G+++ G + + 
Sbjct: 70  RFAGQPLQWKSAADAKRHGIHVIHQELVLFPQSTVAENIFAGAEPRTRIGVLDHGRMNRD 129

Query: 132 ALTLLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLM 191
           A  LL  L   +D +E+VG LS+  +Q+VEIAKA++    V+  DEPT+ ++ +E+  L 
Sbjct: 130 AQALLGELGVRLDSRERVGNLSVADQQMVEIAKAMAGETRVLILDEPTAVIAGKEVQLLF 189

Query: 192 AIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGR 251
           A +  LR +G  ++Y+SHR++E+F +C+ VTV KDGR V T ++++  T DQLV  MVGR
Sbjct: 190 ARVRALRAKGVAIVYISHRLDEIFELCDRVTVMKDGRKVAT-QSVANTTRDQLVRLMVGR 248

Query: 252 DIQDIYDYRPRERGDV--ALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRL 309
           +++DIY  +P     V   L+V GL         S  V  GEI+G+ G+VG+GRTEL   
Sbjct: 249 EMKDIYPDKPILAPGVPNVLEVNGLCVGNRVVDASLTVRAGEIVGIAGMVGSGRTELAAG 308

Query: 310 LSGLERQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARP 369
           + G  R   G++ +        +PR AI  G+    EDRK +G++ L  V +N+  +   
Sbjct: 309 IFGALRAHRGTVDIGGTRRTRMTPRTAIRLGLGFVTEDRKSQGLLMLLDVAQNVTATTLA 368

Query: 370 SHSTLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVL 429
             S  G L+R   ER  A   I   ++        +  LSGGNQQK ++ RW+ +  +VL
Sbjct: 369 QVSRFG-LMRPALERAAAQAAINEYRIAGAHPAGGVATLSGGNQQKVLISRWVRVCKRVL 427

Query: 430 LLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGEL 489
           +LDEPTRG+D+GAKAEIY+++  L + G+ ++++SS+L EV+G+SDR+LV+ EG + GE+
Sbjct: 428 ILDEPTRGVDVGAKAEIYRVMRELTSRGLGILMISSELQEVIGMSDRVLVMREGRINGEV 487

Query: 490 SRDQANESNLLQLA 503
           S +Q  E ++++LA
Sbjct: 488 SGEQMTEHDIMRLA 501



 Score = 75.1 bits (183), Expect = 6e-18
 Identities = 60/227 (26%), Positives = 110/227 (48%), Gaps = 6/227 (2%)

Query: 281 EPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLERQREGSLVLHDKELKLRSPRDAIAAG 340
           + VS  V  GEI  L G  GAG++ L ++++G+     G +    + L+ +S  DA   G
Sbjct: 29  DQVSLGVRAGEIHALVGENGAGKSTLTKIMAGVYAPDSGEIRFAGQPLQWKSAADAKRHG 88

Query: 341 VLLCPEDRKKEGIIPLGSVGENINISARPSHSTLGCLLRGDWERGNADKQIKSLKVKTPT 400
           + +  ++     + P  +V ENI   A P  + +G L  G   R +A   +  L V+  +
Sbjct: 89  IHVIHQELV---LFPQSTVAENIFAGAEP-RTRIGVLDHGRMNR-DAQALLGELGVRLDS 143

Query: 401 AGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAV 460
             +++  LS  +QQ   + + ++   +VL+LDEPT  I       ++  +  L A G+A+
Sbjct: 144 R-ERVGNLSVADQQMVEIAKAMAGETRVLILDEPTAVIAGKEVQLLFARVRALRAKGVAI 202

Query: 461 IVVSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPRQ 507
           + +S  L E+  + DR+ V+ +G      S        L++L + R+
Sbjct: 203 VYISHRLDEIFELCDRVTVMKDGRKVATQSVANTTRDQLVRLMVGRE 249


Lambda     K      H
   0.320    0.138    0.391 

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: 673
Number of extensions: 36
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 514
Length of database: 517
Length adjustment: 35
Effective length of query: 479
Effective length of database: 482
Effective search space:   230878
Effective search space used:   230878
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: 52 (24.6 bits)

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

Downloads

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

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:

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
the source code
instructions for running GapMind on your computer

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