GapMind for catabolism of small carbon sources

 

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

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate AO356_28510 AO356_28510 xylose transporter

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28510
          Length = 518

 Score =  322 bits (825), Expect = 2e-92
 Identities = 204/510 (40%), Positives = 303/510 (59%), Gaps = 20/510 (3%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPG-GEC 71
           LL +  I KTF GV+AL  +++    GE   L GENGAGKSTLMK+LS  Y      GE 
Sbjct: 5   LLQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPHGTWEGEI 64

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRG-LVARGDMVRA 130
             DGQ ++          G+ +I+QEL+L P+LSVAENI++G  L   G  +    M+  
Sbjct: 65  IWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPAMIHR 124

Query: 131 CAPTLARLGA-DFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRL 189
               +  L   D + +  V+      +QLVEIA+A++ +AR+L++DEP++ L+  E + L
Sbjct: 125 AEALMRELKVPDMNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEVL 184

Query: 190 FALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGR 249
             +IR L+ +G+A +YISH++ E+  + D ++V+RDG  + T     +    ++  MVGR
Sbjct: 185 LDIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMTDMDIPKIITQMVGR 244

Query: 250 DLSGFY-TKTH--GQAVEREVMLSVRDVADGRR--VKGCSFDLRAGEVLGLAGLVGAGRT 304
           ++S  Y T+ H  G+ +     ++  DV + RR  V   SF L+ GE+LG+AGLVGAGRT
Sbjct: 245 EMSNLYPTEPHDIGEVIFEARHVTCYDVDNPRRKRVDDISFVLKRGEILGIAGLVGAGRT 304

Query: 305 ELARLVFGA-DARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLD 363
           EL   +FGA   R  GEV +           +    P ++I AG+  + EDRK QG+  D
Sbjct: 305 ELVSALFGAYPGRYEGEVWLNGQQ-------IDTRTPLKSIRAGLCMVPEDRKRQGIIPD 357

Query: 364 QSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKV 423
             V +NI L V    +  L R++  A      + I  + ++ A   + + +LSGGNQQK 
Sbjct: 358 LGVGQNITLAVLDNYSK-LTRIDAEAELGSIDKEIARMHLKTASPFLPITSLSGGNQQKA 416

Query: 424 MLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDR 483
           +L+++L  +PRVLILDEPTRGVD+GAK EIY+L+ ALA  GV+I+M+SSEL EV+G+ DR
Sbjct: 417 VLAKMLLTKPRVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEVLGVSDR 476

Query: 484 VLVMREGTLAGEVRPAGSAAETQERIIALA 513
           VLV+ +G L G+     +   TQE+++A A
Sbjct: 477 VLVIGDGQLRGDFI---NHELTQEQVLAAA 503


Lambda     K      H
   0.320    0.136    0.382 

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: 599
Number of extensions: 29
Number of successful extensions: 9
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: 540
Length of database: 518
Length adjustment: 35
Effective length of query: 505
Effective length of database: 483
Effective search space:   243915
Effective search space used:   243915
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