GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araUsh in Burkholderia phytofirmans PsJN

Align Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale)
to candidate BPHYT_RS23870 BPHYT_RS23870 LacI family transcription regulator

Query= uniprot:A0KWY4
         (313 letters)



>FitnessBrowser__BFirm:BPHYT_RS23870
          Length = 328

 Score =  285 bits (728), Expect = 1e-81
 Identities = 158/313 (50%), Positives = 205/313 (65%), Gaps = 9/313 (2%)

Query: 6   IITALGLWAVSATCAYAT----TVGFSQVGSESGWRTSFSEAVKAEAKQRGIDLKFADAQ 61
           +    G   ++   AYA     T+GF+QVG+ES WRT+ +E++K+ A    I LKF+DAQ
Sbjct: 17  LCAGFGALTLATPGAYAQDKQITLGFAQVGAESAWRTANTESIKSAAADAKIKLKFSDAQ 76

Query: 62  QKQENQIKAVRSFIAQGVDAIIIAPVVETGWKPVLKEAKRAKIPVVIVDRNIKVDDDSLF 121
           QKQENQIKA+RS+IAQ VD I  +PVVE+GW+PVL+EAK AKIPV++ DRNI   D SL+
Sbjct: 77  QKQENQIKAIRSYIAQKVDVIAFSPVVESGWEPVLREAKAAKIPVILTDRNIDTKDTSLY 136

Query: 122 LTRIASDFSEEGRKIGQWLMD---KTQGNCDIAELQGTVGATAAIDRAAGFNQVIANYPN 178
           +T I SDF EEGR+ G WL D     QG  +IAELQGTVG+  A DR +G  +VI + P 
Sbjct: 137 VTMIGSDFLEEGRRGGHWLEDHFKNDQGPINIAELQGTVGSAPANDRHSGLVEVIKSDPK 196

Query: 179 AKIVRSQTGEFTRAKGKEVMEGFLKAQNGQPLCAVWSHNDEMALGAVQAIKEAGLKPGKD 238
            KI+ SQ+G+FT A GK+VME F+K   G  +  V++HND+MALGA+QA++EAG+ PGKD
Sbjct: 197 FKIIASQSGDFTLAGGKQVMEAFIKTY-GNKINVVYAHNDDMALGAIQAMEEAGMHPGKD 255

Query: 239 ILIVSVDGVPDYFKAMADGDVNATVELSPYLGGPAFDAIDAYLKGNKDQAKLISTTGDVF 298
           I +VS D     F+AMA G +N  VE SP LG     A+   + G K   K I T   VF
Sbjct: 256 ITVVSFDATKGGFQAMAAGKMNVDVECSPLLGPQLMSAVKDVVAG-KSLPKRILTEETVF 314

Query: 299 TQETAAAEYEKRR 311
               AA     R+
Sbjct: 315 PMSVAAQTLPTRK 327


Lambda     K      H
   0.316    0.131    0.376 

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: 270
Number of extensions: 10
Number of successful extensions: 3
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: 313
Length of database: 328
Length adjustment: 28
Effective length of query: 285
Effective length of database: 300
Effective search space:    85500
Effective search space used:    85500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 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