GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16925 in Burkholderia phytofirmans PsJN

Align Arabinose ABC transporter permease (characterized, see rationale)
to candidate BPHYT_RS01810 BPHYT_RS01810 sugar ABC transporter permease

Query= uniprot:A0A161GM94
         (322 letters)



>FitnessBrowser__BFirm:BPHYT_RS01810
          Length = 319

 Score =  200 bits (509), Expect = 3e-56
 Identities = 126/310 (40%), Positives = 186/310 (60%), Gaps = 19/310 (6%)

Query: 26  MLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVIA 85
           +LLA   + V   +  ++F S  N+       S   + +  M + + +G  DLSVG+V A
Sbjct: 7   ILLALAALVVFGLVRYEHFGSAYNITSFWRYNSMFALISVGMAFVIITGGIDLSVGTVAA 66

Query: 86  CAGVVAAVVMRDTNSVFLGISAALV---MGLIVGLINGIVIAKLRVNALITTLATMQIVR 142
            A VVAA+      SV+ G  A L     GL VG++NG++I +L++   I TLAT     
Sbjct: 67  LASVVAALT-----SVYGGWVAVLAGCGAGLAVGVLNGLIITRLKILPFIVTLATSLGAH 121

Query: 143 GLAYIFANGKAVGVSQESFFV-FGNGQMFGVPVPILITIVCFLFFGWL-LNYTTYGRNTM 200
           G+A +     AV ++ ES F  FG G +FG+P+P ++ +V  +  GWL L  T +GR+++
Sbjct: 122 GVALLLGKNDAVSIAAESNFGNFGQGDLFGLPIPGIVAVVAAV-AGWLALRSTRFGRHSL 180

Query: 201 AIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVISA 260
           AIGG++EAA L G+NVDRT ++ +AV G++  +AGVILA++  +GQP  G G+EL  ISA
Sbjct: 181 AIGGSEEAARLMGLNVDRTLVMAYAVSGLLAGMAGVILAAQFGAGQPNEGVGWELFAISA 240

Query: 261 CVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKN------IDTFYQYVIRGSILLLAV 314
            VLGG  L+GG G I   IAGVL+L ++ N +N +N      +  ++Q VIRG  LLL +
Sbjct: 241 VVLGGTLLTGGEGSIAMTIAGVLLLGLVFNLLNFENGLGFISLSAYWQSVIRGVFLLLVI 300

Query: 315 VIDR--LKQR 322
           V+    LKQR
Sbjct: 301 VLQARVLKQR 310


Lambda     K      H
   0.330    0.144    0.420 

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: 288
Number of extensions: 18
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: 322
Length of database: 319
Length adjustment: 28
Effective length of query: 294
Effective length of database: 291
Effective search space:    85554
Effective search space used:    85554
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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