GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcB in Paraburkholderia bryophila 376MFSha3.1

Align Xylose ABC transporter, periplasmic xylose-binding protein XylF (characterized, see rationale)
to candidate H281DRAFT_04150 H281DRAFT_04150 monosaccharide ABC transporter substrate-binding protein, CUT2 family

Query= uniprot:A0A0C4Y591
         (325 letters)



>FitnessBrowser__Burk376:H281DRAFT_04150
          Length = 317

 Score =  165 bits (418), Expect = 1e-45
 Identities = 107/292 (36%), Positives = 166/292 (56%), Gaps = 10/292 (3%)

Query: 29  AAPASAAAQRPLKKVGVTLGSLGNPYFVALAHGAEAAAKKINPDAKVTVLSADYDLNKQF 88
           A PA+ AA  PLK +G+T   L NPYFV +      AA      A V V  A +D++KQ 
Sbjct: 32  AVPAAQAA--PLK-IGMTFQELNNPYFVTMQKALNDAAASTG--ATVIVTDAHHDVSKQV 86

Query: 89  SHIDSFIVSKVDLILINAADARAIEPAVRKARKAGIVVVAVDVAAAG-ADATVQTDNTRA 147
           S ++  +  K+D++L+N  D+  I+ AV  A+KAG+VVVAVD  A G  D+ V + N  A
Sbjct: 87  SDVEDMLQKKIDILLVNPTDSTGIQSAVTSAKKAGVVVVAVDANANGPVDSFVGSKNFDA 146

Query: 148 GELACAFLAGRLGGRGNLIIQNGPPVSAVLDRVKGCKMVLGKHPGIHVLSDDQDGKGSRE 207
           G++AC +L+  +GG G + I +G PV  +L+RV+GCK  L K PG+  L D Q+GK  R 
Sbjct: 147 GQMACEYLSKSIGGSGEVAILDGIPVVPILERVRGCKAALAKSPGVK-LVDTQNGKQERA 205

Query: 208 GGLNVMQLYLTRFPKIDAVFTINDPQAVGADLAARQLNRGGILIASVDGAPDIEAAL-KA 266
             L+V +  +   P +  VF++ND  ++GA L+A + +   I + SVDGAP+  AA+ K 
Sbjct: 206 TALSVTENMIQAHPNLKGVFSVNDGGSMGA-LSAIESSGKDIKLTSVDGAPEAIAAIQKP 264

Query: 267 NTLVQASASQDPWAIARTAVEIGVGLMHGQAPANRTVLLPPTLVTRANVNEY 318
           N+    +++Q P    R A+ I      G A   + + +   ++ ++N   +
Sbjct: 265 NSKFVETSAQFPADQVRIALGIAYAKKWG-ANVPKAIPVDVKMIDKSNAKGF 315


Lambda     K      H
   0.318    0.132    0.377 

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: 182
Number of extensions: 14
Number of successful extensions: 5
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: 325
Length of database: 317
Length adjustment: 28
Effective length of query: 297
Effective length of database: 289
Effective search space:    85833
Effective search space used:    85833
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 (21.7 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