GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Burkholderia phytofirmans PsJN

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate BPHYT_RS23145 BPHYT_RS23145 putrescine/spermidine ABC transporter ATP-binding protein

Query= TCDB::P31134
         (377 letters)



>FitnessBrowser__BFirm:BPHYT_RS23145
          Length = 387

 Score =  404 bits (1038), Expect = e-117
 Identities = 203/370 (54%), Positives = 269/370 (72%)

Query: 7   RPQAKTRKALTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLA 66
           RP   T+      + I N+ K +    AVD+V+L+I K E+FALLG+SGCGKSTLLRMLA
Sbjct: 17  RPAVTTKSKSDEFVRIENVVKKFGDSTAVDNVNLSIAKNELFALLGSSGCGKSTLLRMLA 76

Query: 67  GFEQPSAGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEI 126
           G E  ++G+I +DG DL+ +PPY RP+NMMFQSYALFPHM+VE NIAFGLKQ+  PK EI
Sbjct: 77  GLETVTSGRIFVDGEDLAAMPPYKRPVNMMFQSYALFPHMSVEANIAFGLKQEGTPKNEI 136

Query: 127 ASRVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRD 186
             RV + L LV M ++A+RKPHQLSGGQ+QRVALARSL KRPKLLLLDEPM ALDKK+R 
Sbjct: 137 KERVADALNLVQMSKYAQRKPHQLSGGQQQRVALARSLVKRPKLLLLDEPMSALDKKIRQ 196

Query: 187 RMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYS 246
           + QLE+V+I+E+V VTCVMVTHDQEEAMTMAGR+A+M+ G+ VQIG P ++YE P +R+S
Sbjct: 197 KTQLELVNIIEKVDVTCVMVTHDQEEAMTMAGRLAVMSEGRIVQIGSPSQVYEFPNSRFS 256

Query: 247 AEFIGSVNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCE 306
           AEFIGS N+FEG +   + D + ++S  L   + V    +    +PV +++RPE+I +  
Sbjct: 257 AEFIGSTNLFEGTVVADEPDHIFVESEELESRIYVSHGITGPLGMPVGISVRPERIKVSL 316

Query: 307 EPPANGCNFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLC 366
           + P    N+A G V  +AY+G  S+YHVRL SG+ + + L ++H   +G P++ D+V + 
Sbjct: 317 DKPTTPHNWARGVVADVAYMGSYSLYHVRLPSGKTVVSNLSSSHLMAEGAPSYNDDVFVY 376

Query: 367 WEVDSCVVLT 376
           W   S VVLT
Sbjct: 377 WSPASGVVLT 386


Lambda     K      H
   0.321    0.137    0.400 

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: 396
Number of extensions: 6
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: 377
Length of database: 387
Length adjustment: 30
Effective length of query: 347
Effective length of database: 357
Effective search space:   123879
Effective search space used:   123879
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: 50 (23.9 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