Alignments for a candidate for HSERO_RS05250 in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Pseudomonas fluorescens GW456-L13

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate PfGW456L13_7 ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_7
          Length = 521

 Score =  271 bits (693), Expect = 4e-77
 Identities = 171/493 (34%), Positives = 266/493 (53%), Gaps = 18/493 (3%)

Query: 20  VPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDI 79
           VP + LR + KR+PG LA D     +A GE+HAL+GENGAGKSTLMKI+ GV   DSG++
Sbjct: 11  VPRLQLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEV 70

Query: 80  LLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFI-DEDELN 138
           +  G+ V +  P QA+ LGIG++ Q  +L   LS AQNI +      AMG       +L 
Sbjct: 71  IWQGQRVSLRNPAQARGLGIGMVFQHFSLFETLSVAQNIAL------AMGAAAGTPKQLE 124

Query: 139 RQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAE 198
            +   +  R  + ++P   V  L++  +Q VEI + L  D R+LI+DEPT+ L   E  +
Sbjct: 125 PKIREVSRRYGMTLEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADD 184

Query: 199 LFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
           LF  +R L A+G  I++ISHK+ E+R +    +V+R G+        E S   +  +MVG
Sbjct: 185 LFVTLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQLARLMVG 244

Query: 259 RALDGEQRIPPDTSRNDVVLEVRGLN------RGRAIRDVSFTLRKGEILGFAGLMGAGR 312
            A +     P  T   D  L+VRGL+       G ++ ++   +R+GEI+G AG+ G G+
Sbjct: 245 EAAELIADYPKVTG-GDACLDVRGLSWHNPDPFGCSLANIDLEVRRGEIVGIAGVAGNGQ 303

Query: 313 TEVARAIFGAD--PLEAGEIIIHGGKAVIKSPADAVAH-GIGYLSEDRKHFGLAVGMDVQ 369
            E+   + G    P  A   I  G + V     DA    G+ ++  +R   G    + + 
Sbjct: 304 DELLALLSGEALLPRNASATIRFGKEPVAHLRPDARRQLGLAFVPAERLGHGAVPELSLA 363

Query: 370 ANIALSSMGR-FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAK 428
            N  L++        G + +  +   A+  +R+  +KTP  +  AR LSGGN QK ++ +
Sbjct: 364 DNALLTAFQHGLVSNGLIQRGKVEALAEEIIRRFGVKTPDSQAPARSLSGGNLQKFILGR 423

Query: 429 WLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVM 488
            +L+   +L    PT G+DVGA + I++ L AL + G AI++IS +L E+ ++S R+  +
Sbjct: 424 EILQQPRLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQISDRLGAL 483

Query: 489 CEGRITGELARAD 501
           C GR++   A  D
Sbjct: 484 CGGRLSALHATVD 496



 Score = 97.8 bits (242), Expect = 8e-25
 Identities = 65/219 (29%), Positives = 111/219 (50%), Gaps = 9/219 (4%)

Query: 292 VSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIG 351
           +  T+  GEI    G  GAG++ + + I+G    ++GE+I  G +  +++PA A   GIG
Sbjct: 32  IDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVIWQGQRVSLRNPAQARGLGIG 91

Query: 352 YLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQ 411
            + +   HF L   + V  NIAL+ MG         +  IRE ++ Y   L       E+
Sbjct: 92  MVFQ---HFSLFETLSVAQNIALA-MGAAAGTPKQLEPKIREVSRRYGMTL-----EPER 142

Query: 412 QARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMI 471
               LS G +Q++ I + L++D  +L  DEPT  +      +++  L  LA +G +I+ I
Sbjct: 143 LVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFVTLRRLAAEGCSILFI 202

Query: 472 SSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQL 510
           S +L EV  + H   V+  GR+ G    A+ + +++ +L
Sbjct: 203 SHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQLARL 241



 Score = 60.1 bits (144), Expect = 2e-13
 Identities = 57/232 (24%), Positives = 98/232 (42%), Gaps = 10/232 (4%)

Query: 37  ALDNCQFELAAGEVHALMGENGAGKSTLMKILSG---VYQRDSGDILLDGKPVEITEPRQ 93
           +L N   E+  GE+  + G  G G+  L+ +LSG   + +  S  I    +PV    P  
Sbjct: 279 SLANIDLEVRRGEIVGIAGVAGNGQDELLALLSGEALLPRNASATIRFGKEPVAHLRPDA 338

Query: 94  AQALGIGIIHQEL---NLMNHLSAAQNIFIG--REPRKAMGLFIDEDELNRQAAAIFARM 148
            + LG+  +  E      +  LS A N  +   +    + GL I   ++   A  I  R 
Sbjct: 339 RRQLGLAFVPAERLGHGAVPELSLADNALLTAFQHGLVSNGL-IQRGKVEALAEEIIRRF 397

Query: 149 RLDM-DPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQ 207
            +   D   P   L+    Q   + + +    R+L+   PT  ++    A + R +  L+
Sbjct: 398 GVKTPDSQAPARSLSGGNLQKFILGREILQQPRLLVAAHPTWGVDVGAAATIHRALIALR 457

Query: 208 AQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGR 259
             G  I+ IS  +DEL QI+DR+  +  G+  A     +T +  +   M G+
Sbjct: 458 DAGAAILVISEDLDELFQISDRLGALCGGRLSALHATVDTRLSDVGGWMAGQ 509


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: 589
Number of extensions: 42
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: 520
Length of database: 521
Length adjustment: 35
Effective length of query: 485
Effective length of database: 486
Effective search space:   235710
Effective search space used:   235710
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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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