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

GapMind for catabolism of small carbon sources

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

Align ABC transporter related (characterized, see rationale)
to candidate H281DRAFT_05270 H281DRAFT_05270 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__Burk376:H281DRAFT_05270
          Length = 539

 Score =  469 bits (1208), Expect = e-137
 Identities = 242/501 (48%), Positives = 335/501 (66%), Gaps = 7/501 (1%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           IL    +SK +PGVKAL+ V  RLF GEVH L+G+NGAGKSTL+ V+TG  + D G I  
Sbjct: 35  ILATTGVSKTFPGVKALQRVDFRLFPGEVHTLMGQNGAGKSTLINVLTGVIAPDTGTIRL 94

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123
            GE   F +P +A+ AG+ T+YQEVNL PNL+VA+N+F G +PRR G I +  +   A+A
Sbjct: 95  AGEVVAFASPQEAEAAGVRTLYQEVNLCPNLSVAENIFAGRQPRRFGAIDWPDIKRRAQA 154

Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183
            L +  + +DV+  L  Y IAVQQ++AIAR +++ A+VL+LDEPT+SLD  EV  LF IL
Sbjct: 155 ALARLDISLDVTRSLDAYPIAVQQMVAIARALSVDARVLILDEPTSSLDDSEVAQLFKIL 214

Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243
             LK  G+AI+F+THF++Q Y ISDRITV+RNG+  GEYL   L   +L+  M+G     
Sbjct: 215 RHLKQSGIAILFVTHFIEQTYAISDRITVMRNGEREGEYLARNLSADQLVAKMVGHERMS 274

Query: 244 QLVDKQEKERTV-------TRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSG 296
           + + +   E +         RA +  + L  V  +G++Q ++L V +GQ +GLAGLLGSG
Sbjct: 275 ERLREAAHEASAPGGTERGERAASAFIELRGVGKRGTLQPIDLNVERGQILGLAGLLGSG 334

Query: 297 RSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIREN 356
           R+E    +FG D  DSG++ + G+ + L  P DA+  GIA C EDRK +GI+  LSIREN
Sbjct: 335 RTETARLLFGADRADSGTMLVDGKPVRLRSPHDAVRHGIAYCAEDRKKEGIVADLSIREN 394

Query: 357 IILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLA 416
           I+LALQAR GWWR +S  R +E+A  +I++L I   DA++PI  LSGGNQQK +LARWLA
Sbjct: 395 ILLALQARRGWWRKISRQRARELADLWIERLGIKASDAEQPIGLLSGGNQQKALLARWLA 454

Query: 417 IEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDR 476
            +P LL+LDEPTRGID+ A  +I+  +  LC  G+S+L  SSE+ E++  S++V VLRDR
Sbjct: 455 TDPKLLILDEPTRGIDVAAKFDIMDRLLALCANGLSILFISSEISEVLRVSHRVAVLRDR 514

Query: 477 YAVRELSGAELTSQHVMQAIA 497
             + E+ G      ++ + IA
Sbjct: 515 RKIAEVEGKASNEDNIYRLIA 535


Lambda     K      H
   0.319    0.136    0.377 

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: 675
Number of extensions: 23
Number of successful extensions: 6
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: 499
Length of database: 539
Length adjustment: 35
Effective length of query: 464
Effective length of database: 504
Effective search space:   233856
Effective search space used:   233856
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.

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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
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