GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Pseudomonas fluorescens FW300-N2C3

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate AO356_28510 AO356_28510 xylose transporter

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28510
          Length = 518

 Score =  349 bits (895), Expect = e-100
 Identities = 208/508 (40%), Positives = 321/508 (63%), Gaps = 27/508 (5%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDS--GRVM 62
           L+ + I K F GV+AL+G+   V  G+  GL GENGAGKSTL+K+L   Y   +  G ++
Sbjct: 6   LQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPHGTWEGEII 65

Query: 63  IDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQ---LP----NSLGWVNKR 115
            DG  ++  S + + AAGI +IHQEL  VPDL+VAEN+ +G    LP    N    +++ 
Sbjct: 66  WDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPAMIHRA 125

Query: 116 EAKRFVRE-RLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHR 174
           EA   +RE ++  M V+L     + +     +Q+VEI KAL + AR++ LDEP+S+L+  
Sbjct: 126 EA--LMRELKVPDMNVSLP----VSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRS 179

Query: 175 ETEVLFKLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIV 234
           E EVL  ++RDL+A   A +YISH++DE+  +CD  ++ RDG+ IA+   +  +    I+
Sbjct: 180 EIEVLLDIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIAT-TAMTDMDIPKII 238

Query: 235 SEMVGREISDIYNYSARPLGEVRFAAKGIEGHALAQPA-------SFEVRRGEIVGFFGL 287
           ++MVGRE+S++Y      +GEV F A+ +  + +  P        SF ++RGEI+G  GL
Sbjct: 239 TQMVGREMSNLYPTEPHDIGEVIFEARHVTCYDVDNPRRKRVDDISFVLKRGEILGIAGL 298

Query: 288 VGAGRSELMHLVYGA-DHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMA 346
           VGAGR+EL+  ++GA   +  GE+ L+G+ I  R+  ++IR G+ + PEDRK +GI+   
Sbjct: 299 VGAGRTELVSALFGAYPGRYEGEVWLNGQQIDTRTPLKSIRAGLCMVPEDRKRQGIIPDL 358

Query: 347 TVSENINISCRRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAI 406
            V +NI ++   +Y ++   +D + E  + D+ I  + +KT S    I  LSGGNQQKA+
Sbjct: 359 GVGQNITLAVLDNYSKLTR-IDAEAELGSIDKEIARMHLKTASPFLPITSLSGGNQQKAV 417

Query: 407 LSRWLAEPDLKVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDR 466
           L++ L     +V+ILDEPTRG+DVGAK+EIY ++  LA  G +I+M+SSEL EVLGVSDR
Sbjct: 418 LAKMLLTKP-RVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEVLGVSDR 476

Query: 467 IVVMRQGRISGELTRKDATEQSVLSLAL 494
           ++V+  G++ G+    + T++ VL+ AL
Sbjct: 477 VLVIGDGQLRGDFINHELTQEQVLAAAL 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: 665
Number of extensions: 36
Number of successful extensions: 12
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 512
Length of database: 518
Length adjustment: 35
Effective length of query: 477
Effective length of database: 483
Effective search space:   230391
Effective search space used:   230391
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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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:

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:

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:

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:

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