GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Burkholderia phytofirmans PsJN

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate BPHYT_RS35680 BPHYT_RS35680 sugar ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__BFirm:BPHYT_RS35680
          Length = 360

 Score =  304 bits (779), Expect = 2e-87
 Identities = 175/376 (46%), Positives = 233/376 (61%), Gaps = 27/376 (7%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           MA + L  + K Y     GD   V  I LDIDDGEF+VLVGPSGCGKST +RM+AGLE +
Sbjct: 1   MAAVQLSGIFKRY-----GDTQVVHGIDLDIDDGEFVVLVGPSGCGKSTLMRMVAGLEEI 55

Query: 61  TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFG---LEESTGLPDDEIR 117
           + G+L +     N ++ Q R+I+MVFQSYALYPH SV  N++FG    +ES+       +
Sbjct: 56  SGGDLMIGGTRANSLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESSA----SFK 111

Query: 118 QRVEETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAE 177
            R+E    ML +   LDR P  LSGGQ+QRVA+GRA+VR+P +FL DEPLSNLDAKLR +
Sbjct: 112 PRIEAAAKMLNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQ 171

Query: 178 MRTELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVA 237
           MRTE++ L   L  T +YVTHDQ EAMTM DR+ V++ G ++Q+G PL+ Y  P NLFVA
Sbjct: 172 MRTEIKALHQRLKNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVA 231

Query: 238 GFIGEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGA-------SGLTLGIRPEDVT 290
            F+G PSMN  +G ++    +G G    L+G     L GA       + +TLG+RPE + 
Sbjct: 232 SFLGSPSMNFAEGVIASRA-QGQGLALNLTGGGEIVLEGAPASAVVGAKVTLGVRPEHI- 289

Query: 291 VGERRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSF 350
             E  +       EV VVEP G E  ++ +      G+ +  TT  +S++E G R T+  
Sbjct: 290 --ETMTPTPDATMEVEVVEPTGAETHLYGKI----GGSTWCVTTRQRSKIEPGQRVTLRL 343

Query: 351 PEDAIHLFDGETGDAL 366
           P + IHLFD E+G  L
Sbjct: 344 PAEHIHLFDTESGRRL 359


Lambda     K      H
   0.316    0.136    0.384 

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: 406
Number of extensions: 23
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: 383
Length of database: 360
Length adjustment: 30
Effective length of query: 353
Effective length of database: 330
Effective search space:   116490
Effective search space used:   116490
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: 42 (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.

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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