Alignments for a candidate for PS417_11890 in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Burkholderia phytofirmans PsJN

Align Inositol transport system ATP-binding protein (characterized)
to candidate BPHYT_RS20740 BPHYT_RS20740 D-ribose transporter ATP binding protein

Query= reanno::WCS417:GFF2332
         (517 letters)



>FitnessBrowser__BFirm:BPHYT_RS20740
          Length = 503

 Score =  441 bits (1134), Expect = e-128
 Identities = 237/492 (48%), Positives = 327/492 (66%), Gaps = 3/492 (0%)

Query: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82
           L+ +  +SK FPGV AL +VQ  +  G V ALMGENGAGKSTLMKI+AG+Y  D GEI  
Sbjct: 4   LISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEILY 63

Query: 83  RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHM-VNHREMHRCT 141
            G+P+ F++P  AQ  G+ +IHQEL LM H++IA+N++IGRE    L + ++  +++   
Sbjct: 64  EGQPVDFQSPREAQAVGVGIIHQELQLMNHLTIAQNMFIGREPRGRLGLFLDEDKLNAQA 123

Query: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201
            ++LAR+ + LDP   V +L++A +QMVEIAKA+S+DS +LIMDEPTSA+ + E+A LF 
Sbjct: 124 HDILARMHVTLDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAELFR 183

Query: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261
           II DLK +G GI+YI+HKM+E+  IAD V V RDG Y+           ++I MMVGR L
Sbjct: 184 IIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMMVGRTL 243

Query: 262 SQLFPLRETPI-GDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFG 320
           +   P +     G++ L V  L    + +DVSF L  GEILG AGLMG+GRT VA  +FG
Sbjct: 244 TDAAPSQHIANQGEVALEVTRLNAGPLVRDVSFALRKGEILGFAGLMGAGRTEVARAVFG 303

Query: 321 ITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYT 380
             P  SG+I + G    I +P  A+ +G   L+EDRK  GL   +SV  N+ M+ L  + 
Sbjct: 304 ADPIESGEIVVKGVKATIRNPSDAVARGIGYLSEDRKRFGLATGMSVESNIVMSNLRKFL 363

Query: 381 G-NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILD 439
             N F+++  +R         L ++TPS  Q +  LSGGNQQK ++A+WL  +  +L  D
Sbjct: 364 SLNFFLRRTQIRKTAAHFINLLAIRTPSATQEVRLLSGGNQQKIVIAKWLERDCDVLFFD 423

Query: 440 EPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRS 499
           EPTRGIDVGAK+EIY+L+  LA +G A++MISSELPE+L MSDR++VM EG + G L  +
Sbjct: 424 EPTRGIDVGAKSEIYKLLRSLADQGKAIVMISSELPEILRMSDRIVVMCEGRITGELAAA 483

Query: 500 EATQEKVMQLAS 511
            ATQE++MQLA+
Sbjct: 484 GATQERIMQLAT 495



 Score = 99.0 bits (245), Expect = 4e-25
 Identities = 60/225 (26%), Positives = 118/225 (52%), Gaps = 4/225 (1%)

Query: 290 DVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGF 349
           +V F+L AGE+  + G  G+G++ + + + G+    +G+I  +G+ V    P  A   G 
Sbjct: 22  EVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEILYEGQPVDFQSPREAQAVGV 81

Query: 350 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLE 409
            ++ ++ +L      L++ +NM +   P      F+ +  L A   D+  ++ V T    
Sbjct: 82  GIIHQELQLMNH---LTIAQNMFIGREPRGRLGLFLDEDKLNAQAHDILARMHV-TLDPR 137

Query: 410 QCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIM 469
             + +L+   QQ   +A+ L  + R+LI+DEPT  ++    AE++R+I  L   G+ +I 
Sbjct: 138 ALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAELFRIIRDLKKRGVGIIY 197

Query: 470 ISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASGMT 514
           IS ++ E+  ++DRV V+ +GE + T+   + T + ++ +  G T
Sbjct: 198 ISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMMVGRT 242



 Score = 86.3 bits (212), Expect = 2e-21
 Identities = 64/243 (26%), Positives = 109/243 (44%), Gaps = 10/243 (4%)

Query: 24  LEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLR 83
           LE+  ++ G      + DV   +R G +L   G  GAG++ + + + G    ++GEI ++
Sbjct: 260 LEVTRLNAG----PLVRDVSFALRKGEILGFAGLMGAGRTEVARAVFGADPIESGEIVVK 315

Query: 84  GKPIVFETPLAAQKAGIAMIHQE---LNLMPHMSIAENIWIGR-EQLNSLHMVNHREMHR 139
           G       P  A   GI  + ++     L   MS+  NI +    +  SL+    R   R
Sbjct: 316 GVKATIRNPSDAVARGIGYLSEDRKRFGLATGMSVESNIVMSNLRKFLSLNFFLRRTQIR 375

Query: 140 CTAELLARLRINLDPE--EQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVA 197
            TA     L     P   ++V  LS   +Q + IAK +  D D+L  DEPT  I     +
Sbjct: 376 KTAAHFINLLAIRTPSATQEVRLLSGGNQQKIVIAKWLERDCDVLFFDEPTRGIDVGAKS 435

Query: 198 HLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMV 257
            ++ ++  L  QGK IV I+ ++ E+  ++D + V  +G   G   A     + ++ +  
Sbjct: 436 EIYKLLRSLADQGKAIVMISSELPEILRMSDRIVVMCEGRITGELAAAGATQERIMQLAT 495

Query: 258 GRE 260
            RE
Sbjct: 496 QRE 498


Lambda     K      H
   0.320    0.136    0.381 

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: 556
Number of extensions: 22
Number of successful extensions: 8
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: 517
Length of database: 503
Length adjustment: 34
Effective length of query: 483
Effective length of database: 469
Effective search space:   226527
Effective search space used:   226527
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)
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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