Alignments for a candidate for HSERO_RS05250 in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Paraburkholderia bryophila 376MFSha3.1

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__Burk376:H281DRAFT_02712
          Length = 505

 Score =  456 bits (1172), Expect = e-132
 Identities = 240/505 (47%), Positives = 347/505 (68%), Gaps = 9/505 (1%)

Query: 15  SSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQR 74
           S  + VP + +RN+ + FPGV ALD    E+ AGEV AL GENGAGKSTLMKIL+G+Y  
Sbjct: 2   SHVTGVPFLEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAP 61

Query: 75  D-SGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFID 133
           D  G IL++G+ V + +   A+ LG+ II+QEL ++ +L+  +NIF+ REPR  +GL ID
Sbjct: 62  DPGGTILVEGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGL-ID 120

Query: 134 EDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNN 193
              + R+A  + A + +D+DP+T V EL+V +QQM+EIAKAL   S+ +IMDEPTA+L++
Sbjct: 121 RPRMYREAREVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSH 180

Query: 194 AEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTII 253
            E + L  I++ L+ + + +VYISH+++E+ ++ADRV+V+RDG+ + T P+ + + +T++
Sbjct: 181 HETSVLLGIVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLV 240

Query: 254 SMMVGRALDGEQRIPPDTSRNDVVLEVRGLNRGRA------IRDVSFTLRKGEILGFAGL 307
            +MV R L      P   +  D VLEVR L+          IRD+SFTL +GE+LG AGL
Sbjct: 241 RLMVARELSELYGEPQSHASRDPVLEVRALSLKPVRKAEPRIRDISFTLHRGEVLGIAGL 300

Query: 308 MGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMD 367
           +G+GRTE+   IFG      G + I G    I++P DA+  GIG+++EDRK  GL +GM 
Sbjct: 301 VGSGRTEIMEMIFGMRAC-TGSVKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMT 359

Query: 368 VQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIA 427
           V+ N +L+ + R++   F+     RE+ + +VR L IKTP VEQ+   LSGGNQQKIVIA
Sbjct: 360 VRENFSLTHLERYSPFQFVQHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIA 419

Query: 428 KWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLV 487
           KW+ R   +L  DEPTRGIDVGAK+E++ L+  LA +G  +++ISS+L EVL +S R+L 
Sbjct: 420 KWVARSPKVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRILT 479

Query: 488 MCEGRITGELARADATQEKIMQLAT 512
           + EGRI+GEL+RA A+QEK+M LAT
Sbjct: 480 VREGRISGELSRAQASQEKVMALAT 504



 Score = 92.4 bits (228), Expect = 3e-23
 Identities = 76/248 (30%), Positives = 123/248 (49%), Gaps = 20/248 (8%)

Query: 278 LEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRT---EVARAIFGADPLEAGEI 330
           LE+R ++R     +A+  V+  +R GE+L  AG  GAG++   ++   I+  DP   G I
Sbjct: 10  LEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDP--GGTI 67

Query: 331 IIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQ-R 389
           ++ G +  +     A   G+  + ++    G    + V  NI L+   R TR+G +D+ R
Sbjct: 68  LVEGQEVALADSHHARTLGVNIIYQELAVVG---NLTVGENIFLAREPR-TRLGLIDRPR 123

Query: 390 AIREAAQMYVRQLAIKTPSVEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTRGID 447
             REA ++    LA     ++   R+  LS G QQ I IAK L      +  DEPT  + 
Sbjct: 124 MYREAREV----LATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLS 179

Query: 448 VGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKI 507
               S +  ++  L E+  A+V IS  L E+  ++ RV V+ +GR  G    AD T+E +
Sbjct: 180 HHETSVLLGIVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETL 239

Query: 508 MQLATQRE 515
           ++L   RE
Sbjct: 240 VRLMVARE 247


Lambda     K      H
   0.320    0.135    0.372 

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: 677
Number of extensions: 39
Number of successful extensions: 11
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: 520
Length of database: 505
Length adjustment: 35
Effective length of query: 485
Effective length of database: 470
Effective search space:   227950
Effective search space used:   227950
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