GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16935 in Burkholderia phytofirmans PsJN

Align L-arabinose-binding periplasmic protein; Short=ABP; Flags: Precursor (characterized, see rationale)
to candidate BPHYT_RS19715 BPHYT_RS19715 ATPase

Query= uniprot:B2SYR6
         (332 letters)



>FitnessBrowser__BFirm:BPHYT_RS19715
          Length = 334

 Score =  333 bits (855), Expect = 3e-96
 Identities = 165/330 (50%), Positives = 224/330 (67%), Gaps = 1/330 (0%)

Query: 1   MKRRIFLTLAAAATGVLFNAPVAQAAD-PVKIGFLVKQPEEPWFQDEWKFAEIAAKEKGF 59
           ++R     +AAAA    F   ++  AD P+K+GFLVK PE+ WF +E K A    ++ GF
Sbjct: 5   LRRLTLSAMAAAALAAPFAMQLSAHADAPLKVGFLVKMPEQAWFINEQKAASALGQKDGF 64

Query: 60  TLVKIGAPSGEKVMSAIDNLSAQKAQGFVICTPDVKLGPGIVAKAKADGLKMMTVDDRLV 119
           ++V IG P GEKV++AIDNL AQ A+GFVIC PDV+LGP I A+AK   +K +TVDD+LV
Sbjct: 65  SVVNIGTPDGEKVLAAIDNLGAQGAKGFVICAPDVRLGPAIQARAKRYNMKFVTVDDQLV 124

Query: 120 DGAGKPIASVPHMGISAYNIGKQVGDGLAAEIKKRGWDMKDVGAIDVTYEQLPTAHDRTS 179
           D  GKP+ +VPH+G+SA+ IG QVG  ++ E+K+RGW  ++VGA+ +T  +LPTA  RT 
Sbjct: 125 DSTGKPLPNVPHLGMSAFKIGNQVGTAISEEMKRRGWKPEEVGALRITNYELPTAKLRTD 184

Query: 180 GATDALIAAGFPKANIVMAPQAKTDTENAFNAANIALTKNPQFKHWVAYALNDEGVLGAV 239
           GAT +L+A GF K NI  APQ  TD E  FNA++  L ++P  K WV +ALN+E VLG V
Sbjct: 185 GATQSLLAGGFKKENIFDAPQKTTDDEGGFNASSPVLAQHPNIKKWVIFALNEESVLGGV 244

Query: 240 RAAEGRGFKADNMIGIGIGGSDSALNEFKKPSPTGFYGTVIISPKRHGEETSTLMYDWIT 299
           RA E     A ++IG+GI G+  A  EF+K  PTGFYGT+ +S   HG+E++  + +WI 
Sbjct: 245 RATEQLHIPAADVIGVGINGAGEAFAEFQKKEPTGFYGTIAVSSTMHGKESTENLVEWIK 304

Query: 300 QGKAPPPLTLTTGMLATRDNVADVRQKMGL 329
            GK PP  T TTG L  R N  DVR+++G+
Sbjct: 305 DGKQPPADTQTTGKLMVRSNWQDVRKELGI 334


Lambda     K      H
   0.316    0.133    0.391 

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: 358
Number of extensions: 17
Number of successful extensions: 1
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: 332
Length of database: 334
Length adjustment: 28
Effective length of query: 304
Effective length of database: 306
Effective search space:    93024
Effective search space used:    93024
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: 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