GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG' in Burkholderia phytofirmans PsJN

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate BPHYT_RS05035 BPHYT_RS05035 sugar ABC transporter permease

Query= uniprot:A8LLL4
         (385 letters)



>FitnessBrowser__BFirm:BPHYT_RS05035
          Length = 285

 Score =  120 bits (302), Expect = 4e-32
 Identities = 68/215 (31%), Positives = 109/215 (50%), Gaps = 3/215 (1%)

Query: 172 EGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALI 231
           +GM   F N++ + IPA +I  ++ AF  Y L    F G   +  +I+    +P Q  L+
Sbjct: 72  DGMQPFFMNSVRMVIPAVLISSIIGAFNGYVLTHWRFRGADPIFTMILVGCFIPFQAILL 131

Query: 232 PLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIF 291
           P+      +G+     G  + H  +G+       RN+ V +P ++++ A++DGA  F IF
Sbjct: 132 PMARFEGFLGLSNTTTGLVVVHVIYGIAFTTMFFRNFYVSIPAELVKAARIDGAGFFTIF 191

Query: 292 TKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFL-IDATGQTTVMTNQIVELLGTRGGNW 350
           TKI+LP+S P      I+QF   WND L   VF  +D+   T  + N +    G +  N 
Sbjct: 192 TKILLPVSLPIFMVCLIWQFTQIWNDFLFGIVFSGVDSMPITVALNNLVNTSTGVKEYNV 251

Query: 351 EILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385
           ++    A ++    LLV+    R+ VRGL AG+VK
Sbjct: 252 DM--AGAIIAALPTLLVYIIAGRYFVRGLTAGAVK 284


Lambda     K      H
   0.323    0.138    0.419 

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: 274
Number of extensions: 14
Number of successful extensions: 2
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: 385
Length of database: 285
Length adjustment: 28
Effective length of query: 357
Effective length of database: 257
Effective search space:    91749
Effective search space used:    91749
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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