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_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__Burk376:H281DRAFT_02712
          Length = 505

 Score =  401 bits (1031), Expect = e-116
 Identities = 220/500 (44%), Positives = 331/500 (66%), Gaps = 17/500 (3%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPD-SGRVMI 63
           L   NI + FPGV+ALD V+ ++  G+V  L GENGAGKSTL+KIL G Y PD  G +++
Sbjct: 10  LEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTILV 69

Query: 64  DGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNS-LGWVNKREAKRFVR 122
           +G EV    +  +   G+ +I+QEL  V +LTV EN+ L + P + LG +++    R  R
Sbjct: 70  EGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRMYREAR 129

Query: 123 ERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKL 182
           E L  + + +DP  ++ +LS+ Q+QM+EI KAL   ++ I +DEPT+SLSH ET VL  +
Sbjct: 130 EVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLLGI 189

Query: 183 VRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREI 242
           V+ LR  N A++YISHR++EI+EL D  T+ RDGR + + P +  +TR+T+V  MV RE+
Sbjct: 190 VKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAP-IADMTRETLVRLMVAREL 248

Query: 243 SDIY-----NYSARPLGEVRFAAKGIEGHALAQP----ASFEVRRGEIVGFFGLVGAGRS 293
           S++Y     + S  P+ EVR  A  ++    A+P     SF + RGE++G  GLVG+GR+
Sbjct: 249 SELYGEPQSHASRDPVLEVR--ALSLKPVRKAEPRIRDISFTLHRGEVLGIAGLVGSGRT 306

Query: 294 ELMHLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENIN 353
           E+M +++G      G + ++GKP+ +R+  +AIR GI    EDRK +G++   TV EN +
Sbjct: 307 EIMEMIFGM-RACTGSVKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMTVRENFS 365

Query: 354 ISCRRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAE 413
           ++    Y     F+   +E E+  RF+++L IKTP   QK+  LSGGNQQK ++++W+A 
Sbjct: 366 LTHLERYSPF-QFVQHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIAKWVAR 424

Query: 414 PDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQG 473
              KV+I+DEPTRGIDVGAK E++ +I +LA  G  +++ISS+L EVL VSDRI+ +R+G
Sbjct: 425 SP-KVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRILTVREG 483

Query: 474 RISGELTRKDATEQSVLSLA 493
           RISGEL+R  A+++ V++LA
Sbjct: 484 RISGELSRAQASQEKVMALA 503



 Score = 89.4 bits (220), Expect = 3e-22
 Identities = 71/256 (27%), Positives = 126/256 (49%), Gaps = 14/256 (5%)

Query: 252 PLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHL---VYGADHKKGG 308
           P  E+R  ++   G       + E+R GE++   G  GAG+S LM +   +Y  D   GG
Sbjct: 8   PFLEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPD--PGG 65

Query: 309 ELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLD 368
            +L++G+ + +  +  A   G+ +  +   E  +V   TV ENI ++ R    R+G+ +D
Sbjct: 66  TILVEGQEVALADSHHARTLGVNIIYQ---ELAVVGNLTVGENIFLA-REPRTRLGL-ID 120

Query: 369 RKKEAETADRFIKLLKIKT-PSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRG 427
           R +    A   +  + +   P+ R  +  LS G QQ   +++ L     K +I+DEPT  
Sbjct: 121 RPRMYREAREVLATIDMDIDPATR--VSELSVGQQQMIEIAKALCARS-KAIIMDEPTAS 177

Query: 428 IDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQ 487
           +       +  ++ +L ER  A+V IS  L E+  ++DR+ V+R GR  G     D T +
Sbjct: 178 LSHHETSVLLGIVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRE 237

Query: 488 SVLSLALPQSSTALPG 503
           +++ L + +  + L G
Sbjct: 238 TLVRLMVARELSELYG 253


Lambda     K      H
   0.320    0.136    0.385 

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: 625
Number of extensions: 34
Number of successful extensions: 12
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: 512
Length of database: 505
Length adjustment: 34
Effective length of query: 478
Effective length of database: 471
Effective search space:   225138
Effective search space used:   225138
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