Alignments for a candidate for rbsA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Pseudomonas fluorescens GW456-L13

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate PfGW456L13_7 ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_7
          Length = 521

 Score =  256 bits (653), Expect = 2e-72
 Identities = 152/480 (31%), Positives = 255/480 (53%), Gaps = 14/480 (2%)

Query: 5   LQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWL 64
           LQL+ I K +PG  A     L + PG + AL+GENGAGKST+MK++ G+   D+G ++W 
Sbjct: 14  LQLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVIWQ 73

Query: 65  GKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEADK 124
           G+  +   P  ++  GIG++ Q  +L   L++A+NI L         K     +  +  +
Sbjct: 74  GQRVSLRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAGTPK----QLEPKIRE 129

Query: 125 LLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVI 184
           +  +  +  + ++LV  LSIG++Q VEI + L  + +++I+DEPT  LT  E + LF  +
Sbjct: 130 VSRRYGMTLEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFVTL 189

Query: 185 RELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLED 244
           R L ++G  I++ISH++ E+  +C   TV R G+       A  ++  L  +MVG   E 
Sbjct: 190 RRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQLARLMVGEAAEL 249

Query: 245 QYPHLDKAPGDIRLKVDNLC-------GPGVNDVSFTLRKGEILGVSGLMGAGRTELMKV 297
              +     GD  L V  L        G  + ++   +R+GEI+G++G+ G G+ EL+ +
Sbjct: 250 IADYPKVTGGDACLDVRGLSWHNPDPFGCSLANIDLEVRRGEIVGIAGVAGNGQDELLAL 309

Query: 298 LYGA--LPRTSGYVTLDGHEVVTRSPQDGLAN-GIVYISEDRKRDGLVLGMSVKENMSLT 354
           L G   LPR +      G E V     D     G+ ++  +R   G V  +S+ +N  LT
Sbjct: 310 LSGEALLPRNASATIRFGKEPVAHLRPDARRQLGLAFVPAERLGHGAVPELSLADNALLT 369

Query: 355 ALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRP 414
           A ++   + G ++    +    + IR F VKTP  +     LSGGN QK  + R ++ +P
Sbjct: 370 AFQHGLVSNGLIQRGKVEALAEEIIRRFGVKTPDSQAPARSLSGGNLQKFILGREILQQP 429

Query: 415 KVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLS 474
           ++L+   PT GVDVGA   I++ +   +  G +I+++S ++ E+  +SDR+  +  G LS
Sbjct: 430 RLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQISDRLGALCGGRLS 489



 Score = 85.5 bits (210), Expect = 4e-21
 Identities = 64/226 (28%), Positives = 111/226 (49%), Gaps = 14/226 (6%)

Query: 271 VSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQD--GLANG 328
           +  T+  GEI  + G  GAG++ LMK++YG     SG V   G  V  R+P    GL  G
Sbjct: 32  IDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVIWQGQRVSLRNPAQARGLGIG 91

Query: 329 IVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPS 388
           +V+     +   L   +SV +N++L        A G+ K  + +  + +  R + + T  
Sbjct: 92  MVF-----QHFSLFETLSVAQNIALA----MGAAAGTPKQLEPK--IREVSRRYGM-TLE 139

Query: 389 MEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSI 448
            E+ +  LS G +Q+V I R LM   ++LILDEPT  +      +++  + +  A+G SI
Sbjct: 140 PERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFVTLRRLAAEGCSI 199

Query: 449 ILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
           + +S ++ EV  +     V+  G ++G     + + + L    VG+
Sbjct: 200 LFISHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQLARLMVGE 245



 Score = 52.4 bits (124), Expect = 4e-11
 Identities = 48/231 (20%), Positives = 106/231 (45%), Gaps = 11/231 (4%)

Query: 2   EALLQLKGID--KAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTG--IYTRD 57
           +A L ++G+      P   +L+   L V  G ++ + G  G G+  ++ +L+G  +  R+
Sbjct: 260 DACLDVRGLSWHNPDPFGCSLANIDLEVRRGEIVGIAGVAGNGQDELLALLSGEALLPRN 319

Query: 58  AGTLLWLGKE-TTFTGPKSSQEAGIGIIHQEL---NLIPQLTIAENIFLG--REFVNRFG 111
           A   +  GKE      P + ++ G+  +  E      +P+L++A+N  L   +  +   G
Sbjct: 320 ASATIRFGKEPVAHLRPDARRQLGLAFVPAERLGHGAVPELSLADNALLTAFQHGLVSNG 379

Query: 112 KIDWKTMYAEADKLLAKLNLRFKSDKLVG-DLSIGDQQMVEIAKVLSFESKVIIMDEPTD 170
            I    + A A++++ +  ++    +     LS G+ Q   + + +  + ++++   PT 
Sbjct: 380 LIQRGKVEALAEEIIRRFGVKTPDSQAPARSLSGGNLQKFILGREILQQPRLLVAAHPTW 439

Query: 171 ALTDTETESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIA 221
            +      ++ R +  L+  G  I+ IS  + E+F+I D +     G+  A
Sbjct: 440 GVDVGAAATIHRALIALRDAGAAILVISEDLDELFQISDRLGALCGGRLSA 490


Lambda     K      H
   0.318    0.137    0.380 

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: 576
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: 501
Length of database: 521
Length adjustment: 35
Effective length of query: 466
Effective length of database: 486
Effective search space:   226476
Effective search space used:   226476
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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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