GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Pseudomonas fluorescens FW300-N2E2

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate Pf6N2E2_523 Inositol transport system ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523
          Length = 517

 Score =  400 bits (1027), Expect = e-116
 Identities = 236/505 (46%), Positives = 324/505 (64%), Gaps = 17/505 (3%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72
           LL + N+ K FPGV AL  V+L    G V ALMGENGAGKSTLMKI++G Y  D  GE  
Sbjct: 26  LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPD-AGELR 84

Query: 73  IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGL--VARGDMVRA 130
           + G+ V  D P +A   G+A+I+QEL+L P++S+AENI++GR  Q  GL  V  G+M R 
Sbjct: 85  LRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGRE-QLNGLHMVDHGEMHRC 143

Query: 131 CAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 190
            A  L RL     P   V +LSIA+RQ+VEIA+AV +++ IL+MDEPT+ ++  E   LF
Sbjct: 144 TARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLF 203

Query: 191 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 250
           ++I  L+ +G  I+YI+H+M E+  +AD V V RDG ++G      +   +L+ MMVGR+
Sbjct: 204 SIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRE 263

Query: 251 LSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLV 310
           LS  +     Q +  +++LSVRD++     KG SFDL AGE+LG+AGL+G+GRT +A  +
Sbjct: 264 LSQLFP-VREQPIG-DLVLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAEAI 321

Query: 311 FGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENI 370
           FG    T GE+ +      G  V +    P  AI+ G A LTEDRKL GLF   SV EN+
Sbjct: 322 FGVTPSTGGEILL-----DGQPVRI--SDPHMAIEKGFALLTEDRKLSGLFPCLSVLENM 374

Query: 371 NLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLE 430
            + V     +G G + + A R    +    L ++    +  +  LSGGNQQK +L+R L 
Sbjct: 375 EMAVLPH-YVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLM 433

Query: 431 IQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREG 490
             PR+LILDEPTRG+D+GAK+EIYRLI+ LA  G+A++MISSELPEV+G+ DRV+VM EG
Sbjct: 434 TNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEG 493

Query: 491 TLAGEVRPAGSAAETQERIIALATG 515
            L G +   G A  TQER++ LA+G
Sbjct: 494 DLMGTLN-RGEA--TQERVMQLASG 515


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: 630
Number of extensions: 27
Number of successful extensions: 10
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: 517
Length adjustment: 35
Effective length of query: 505
Effective length of database: 482
Effective search space:   243410
Effective search space used:   243410
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