Alignments for a candidate for BPHYT_RS34245 in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS34245 in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate H281DRAFT_01223 H281DRAFT_01223 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__Burk376:H281DRAFT_01223
          Length = 509

 Score =  322 bits (825), Expect = 2e-92
 Identities = 191/494 (38%), Positives = 278/494 (56%), Gaps = 8/494 (1%)

Query: 9   TSSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDT 68
           TS+VP +E    +K FG   AL+D  + + PGE HAL+G NGAGKSTLV IL G+ +PD+
Sbjct: 5   TSAVPRLELRHASKSFGRVRALSDGDLSLWPGEVHALLGENGAGKSTLVKILAGVHQPDS 64

Query: 69  GEVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPL-RGGVIDWQAM 127
           GE+   G A        A    +A +YQ  T+  DLS+AEN+F+ RQP+ R G I + AM
Sbjct: 65  GELLVDGVARRFATPAQARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRFGRIQYDAM 124

Query: 128 RRDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIK 187
           RR+   LL    +D+R D     LS+  +Q++EIA+ALS  A  +I+DEPTA L   E++
Sbjct: 125 RREVDGLLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLTEVE 184

Query: 188 RLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMT 247
           RLF  + +L+   V  LFI+H L EV+ + Q VT++RD   +     + L  + ++  M 
Sbjct: 185 RLFAIVRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGMTADLNTDAIVSKMV 244

Query: 248 GERGGLAVADAAARGALPADTAVALELKELTGAD-YEGVSFTVKRGEVVGLTGATSSGRT 306
           G      +     +   P   A  L ++ LT    ++ +SF V+ GE+V L G   +GR+
Sbjct: 245 GRD----LETFYPKAERPPGEA-RLSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAGRS 299

Query: 307 SVAEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENAS 366
            VA AI G+     G I + G  L  G   A++  G+  VP+DR  +GL L  S+A NAS
Sbjct: 300 EVARAIFGIDPLDAGQIQIGGKPLADGSPAAAVRAGLALVPEDRRQQGLALELSIARNAS 359

Query: 367 MTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATN 426
           MT+   L + G+     +     +    L + A  P   V  LSGGNQQKVV+ + LATN
Sbjct: 360 MTVLGRLVRHGLITTRSETQLANQWGTRLRLKAGDPNAPVGMLSGGNQQKVVLGKWLATN 419

Query: 427 PNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRV 485
           P VL++ +PT G+DV +K  + S +  +  +G AVL++S EL + L   DRVLVM  GR+
Sbjct: 420 PKVLIIDEPTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGRI 479

Query: 486 AAEFPAGWQDHDLI 499
           +A+      D + I
Sbjct: 480 SADIARAEADEERI 493



 Score = 71.2 bits (173), Expect = 8e-17
 Identities = 63/247 (25%), Positives = 108/247 (43%), Gaps = 14/247 (5%)

Query: 13  PVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVR 72
           P  EA    +         D+S  V  GE  AL G  GAG+S +   + G+   D G+++
Sbjct: 258 PPGEARLSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAGRSEVARAIFGIDPLDAGQIQ 317

Query: 73  FSGAAAPSIADRDAWRERVACVYQ---HSTIIRDLSVAEN--LFINRQPLRGGVIDWQAM 127
             G      +   A R  +A V +      +  +LS+A N  + +  + +R G+I     
Sbjct: 318 IGGKPLADGSPAAAVRAGLALVPEDRRQQGLALELSIARNASMTVLGRLVRHGLIT---- 373

Query: 128 RRDARALLDHWKIDVR-----EDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLD 182
            R    L + W   +R      +A  G LS   +Q V + + L+   + +I+DEPT  +D
Sbjct: 374 TRSETQLANQWGTRLRLKAGDPNAPVGMLSGGNQQKVVLGKWLATNPKVLIIDEPTRGID 433

Query: 183 GDEIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQL 242
                 ++  ++EL R+G+  L IS  L EV  +   V V+ + R       +    E++
Sbjct: 434 VGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGRISADIARAEADEERI 493

Query: 243 IEAMTGE 249
           + A  G+
Sbjct: 494 MAAALGQ 500


Lambda     K      H
   0.318    0.134    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: 632
Number of extensions: 22
Number of successful extensions: 8
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: 510
Length of database: 509
Length adjustment: 34
Effective length of query: 476
Effective length of database: 475
Effective search space:   226100
Effective search space used:   226100
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: 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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Steps (tab-delimited)
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Protein sequences (fasta format)
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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