Alignments for a candidate for BPHYT_RS16930 in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS16930 in Pseudomonas fluorescens GW456-L13

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate PfGW456L13_7 ABC transporter ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_7
          Length = 521

 Score =  243 bits (619), Expect = 2e-68
 Identities = 160/488 (32%), Positives = 251/488 (51%), Gaps = 28/488 (5%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L+   I K +PG  A D +   +  G++H L+GENGAGKSTL+KI+ G    DSG V+  
Sbjct: 14  LQLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVIWQ 73

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124
           G  V   + A +   GI ++ Q       L+VA+N+ L  +  + G   + E K  +RE 
Sbjct: 74  GQRVSLRNPAQARGLGIGMVFQHFSLFETLSVAQNIALA-MGAAAGTPKQLEPK--IREV 130

Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184
               G+ L+P   +  LSI +RQ VEI + L+++ R++ LDEPTS L+ +E + LF  +R
Sbjct: 131 SRRYGMTLEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFVTLR 190

Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244
            L A+  ++++ISH++ E+  LC + T+ R GR +A H      +   +   MVG     
Sbjct: 191 RLAAEGCSILFISHKLGEVRALCHSATVLRGGR-VAGHCVPAECSDQQLARLMVGEAAEL 249

Query: 245 IYNYSARPLGEVRFAAKGIEGH-------ALAQPASFEVRRGEIVGFFGLVGAGRSELMH 297
           I +Y     G+     +G+  H       +LA     EVRRGEIVG  G+ G G+ EL+ 
Sbjct: 250 IADYPKVTGGDACLDVRGLSWHNPDPFGCSLAN-IDLEVRRGEIVGIAGVAGNGQDELLA 308

Query: 298 LVYGADHKKGGELLLDGKPIKVRSAGEAIRH---------GIVLCPEDRKEEGIVAMATV 348
           L+       G  LL       +R   E + H         G+   P +R   G V   ++
Sbjct: 309 LL------SGEALLPRNASATIRFGKEPVAHLRPDARRQLGLAFVPAERLGHGAVPELSL 362

Query: 349 SENINISCRRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILS 408
           ++N  ++  +H L     + R K    A+  I+   +KTP  +   R LSGGN QK IL 
Sbjct: 363 ADNALLTAFQHGLVSNGLIQRGKVEALAEEIIRRFGVKTPDSQAPARSLSGGNLQKFILG 422

Query: 409 RWLAEPDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIV 468
           R + +   ++++   PT G+DVGA   I+  +  L + G AI++IS +L E+  +SDR+ 
Sbjct: 423 REILQQP-RLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQISDRLG 481

Query: 469 VMRQGRIS 476
            +  GR+S
Sbjct: 482 ALCGGRLS 489



 Score = 85.5 bits (210), Expect = 4e-21
 Identities = 62/247 (25%), Positives = 117/247 (47%), Gaps = 11/247 (4%)

Query: 252 PLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELL 311
           P  ++R   K   G          +  GEI    G  GAG+S LM ++YG  H   GE++
Sbjct: 12  PRLQLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVI 71

Query: 312 LDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKK 371
             G+ + +R+  +A   GI +  +      +    +V++NI ++       +G      K
Sbjct: 72  WQGQRVSLRNPAQARGLGIGMVFQ---HFSLFETLSVAQNIALA-------MGAAAGTPK 121

Query: 372 EAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVG 431
           + E   R +      T    + +  LS G +Q+  + R L + D++++ILDEPT  +   
Sbjct: 122 QLEPKIREVSRRYGMTLEPERLVHSLSIGERQRVEIIRCLMQ-DIRLLILDEPTSVLTPQ 180

Query: 432 AKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLS 491
              +++  + +LA  GC+I+ IS +L EV  +     V+R GR++G     + ++Q +  
Sbjct: 181 EADDLFVTLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQLAR 240

Query: 492 LALPQSS 498
           L + +++
Sbjct: 241 LMVGEAA 247



 Score = 61.2 bits (147), Expect = 9e-14
 Identities = 56/231 (24%), Positives = 100/231 (43%), Gaps = 15/231 (6%)

Query: 19  ALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEY---QPDSGRVMIDGNEVRFTSAAS 75
           +L  +  +V  G++ G+ G  G G+  LL +L GE    +  S  +      V      +
Sbjct: 279 SLANIDLEVRRGEIVGIAGVAGNGQDELLALLSGEALLPRNASATIRFGKEPVAHLRPDA 338

Query: 76  SIAAGIAVIHQELQ---YVPDLTVAENLLLGQLPNSL---GWVNKREAKRFVRERLEAMG 129
               G+A +  E      VP+L++A+N LL    + L   G + + + +    E +   G
Sbjct: 339 RRQLGLAFVPAERLGHGAVPELSLADNALLTAFQHGLVSNGLIQRGKVEALAEEIIRRFG 398

Query: 130 VAL-DPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVRDLRA 188
           V   D  A  R LS    Q   + + +L+  R++    PT  +       + + +  LR 
Sbjct: 399 VKTPDSQAPARSLSGGNLQKFILGREILQQPRLLVAAHPTWGVDVGAAATIHRALIALRD 458

Query: 189 DNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVG 239
              A++ IS  +DE++++ D       GR  A H T+     DT +S++ G
Sbjct: 459 AGAAILVISEDLDELFQISDRLGALCGGRLSALHATV-----DTRLSDVGG 504


Lambda     K      H
   0.320    0.136    0.385 

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: 648
Number of extensions: 39
Number of successful extensions: 9
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: 512
Length of database: 521
Length adjustment: 35
Effective length of query: 477
Effective length of database: 486
Effective search space:   231822
Effective search space used:   231822
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)
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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