Alignments for a candidate for HSERO_RS03640 in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Burkholderia phytofirmans PsJN

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__BFirm:BPHYT_RS27185
          Length = 516

 Score =  390 bits (1003), Expect = e-113
 Identities = 215/494 (43%), Positives = 308/494 (62%), Gaps = 6/494 (1%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           +LQ++G+ K F   +AL  + L +  GE+HA+ GENGAGKSTLMK++SG +  D+G +  
Sbjct: 23  ILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEGVVRY 82

Query: 66  DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125
            G PV       ++AAGI +I+QEL + P++SVA N+++  E + R   +D+  + S   
Sbjct: 83  RGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPK-RGPFVDYRTLNSNAQ 141

Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185
             L+++G     S L G LS+A+QQ VEIA+AL   +R++IMDEPT++L+E ET QLF +
Sbjct: 142 RCLQRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFRI 201

Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245
           +R LR  G+AI+YISHR+ E+  + DRVTVLRDG  +            IV  MVGR L 
Sbjct: 202 IRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTVNEIVARMVGRPLD 261

Query: 246 EFYQHQRIAPADAAQLPTVMQVRALAG-GKIRPASFDVRAGEVLGFAGLVGAGRTELARL 304
           + Y  ++  P++      +++VR L   G   P SF++R GE+LGFAGL+GAGRTE AR 
Sbjct: 262 DAYPPRQSTPSNQI----LLRVRDLQRTGVFGPLSFELRKGEILGFAGLMGAGRTETARA 317

Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 364
           +FGA+    G I L   PV I  PR A+R GIAY+ EDRK  GL L M V+AN T+    
Sbjct: 318 IFGAERPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANITLANVR 377

Query: 365 RHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLI 424
             +  G +R      +A   ++ L ++    +     LSGGNQQK+++++WL    ++L 
Sbjct: 378 AISSRGFLRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILF 437

Query: 425 LDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELA 484
            DEPTRG+D+ AK  IY L+ RLA+ GV VV+ISSELPE++G+ DR+ V  EG IT  L 
Sbjct: 438 FDEPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGRITAVLE 497

Query: 485 GAAITQENIMRLAT 498
               +QE I+  A+
Sbjct: 498 TRQTSQEEILHHAS 511



 Score = 97.4 bits (241), Expect = 1e-24
 Identities = 72/234 (30%), Positives = 115/234 (49%), Gaps = 6/234 (2%)

Query: 281 DVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVP 340
           D+ AGEV    G  GAG++ L +++ G      G +   G PV       A  AGIA + 
Sbjct: 45  DLCAGEVHAVCGENGAGKSTLMKIISGQYRADEGVVRYRGAPVQFSSTSDAQAAGIAIIH 104

Query: 341 EDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVG 400
           ++     L   ++VA N  + +A    R   V  R+L   A+  +QR+ + V+ P T VG
Sbjct: 105 QELN---LVPHLSVAEN--IYLAREPKRGPFVDYRTLNSNAQRCLQRIGLNVS-PSTLVG 158

Query: 401 KLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSE 460
            LS   QQ V +A+ L +  +VLI+DEPT  +      ++++++  L + GVA++ IS  
Sbjct: 159 ALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFRIIRELRAGGVAILYISHR 218

Query: 461 LPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPASHSSPT 514
           L E+  I DRV V+R+G        A+ T   I+       +    P   S+P+
Sbjct: 219 LDEMAEIVDRVTVLRDGRHIATSDFASTTVNEIVARMVGRPLDDAYPPRQSTPS 272



 Score = 87.0 bits (214), Expect = 1e-21
 Identities = 61/243 (25%), Positives = 113/243 (46%), Gaps = 9/243 (3%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           LL++R +++    T     +   +R GEI    G  GAG++   + + G   PD G I L
Sbjct: 276 LLRVRDLQR----TGVFGPLSFELRKGEILGFAGLMGAGRTETARAIFGAERPDSGSITL 331

Query: 66  DGRPVALRDPGASRAAGINLIYQEL---AVAPNISVAANVFMGS-ELRTRLGLIDHAAMR 121
              PV +  P  +   GI  + ++     +A ++ V+AN+ + +    +  G +  +   
Sbjct: 332 GDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANITLANVRAISSRGFLRFSEET 391

Query: 122 SRTDAVLRQLGAGFGA-SDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180
           +  +  +R+LG        +A  LS   QQ++ I++ L   SRI+  DEPT  +      
Sbjct: 392 AIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKY 451

Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240
            ++ ++ RL  +G+ ++ IS  + E+  + DR+ V  +G     L   +   E I+    
Sbjct: 452 AIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGRITAVLETRQTSQEEILHHAS 511

Query: 241 GRS 243
           GRS
Sbjct: 512 GRS 514


Lambda     K      H
   0.320    0.135    0.378 

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: 679
Number of extensions: 26
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 521
Length of database: 516
Length adjustment: 35
Effective length of query: 486
Effective length of database: 481
Effective search space:   233766
Effective search space used:   233766
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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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