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_02705 H281DRAFT_02705 monosaccharide ABC transporter substrate-binding protein, CUT2 family

Query= uniprot:A0A0C4Y591
         (325 letters)



>FitnessBrowser__Burk376:H281DRAFT_02705
          Length = 365

 Score =  113 bits (283), Expect = 6e-30
 Identities = 97/314 (30%), Positives = 152/314 (48%), Gaps = 23/314 (7%)

Query: 19  TGAAAQSAPDAAPASAAAQRPLKKVGVTLGSLGNPYFVALAHGAEAAAKKINPDAKVTVL 78
           T   A SAP +AP  A A     KVG ++ +L N +FV L  G E  AK+   D   T  
Sbjct: 43  TSGQAASAPASAPV-ANASGGKTKVGFSVSTLNNAFFVGLKAGVEKGAKEQGFDLVQT-- 99

Query: 79  SADYDLNKQFSHIDSFIVSKVDLILINAADARAIEPAVRKARKAGIVVVAVDVAAAGADA 138
           +A+ D  +Q +   + +   V  +++N  D++AI PAV KA    I V  +D  + G   
Sbjct: 100 NANGDAQQQVNDAINLLSQGVTALVLNPIDSKAIIPAVEKANSMNIPVFMLDRGSDGGKV 159

Query: 139 T--VQTDNTRAGELACAFLAGRL-----GGRGNLIIQNG-PPVSAVLDRVKGCKMVLGKH 190
           T  V +DN   G+ A  ++A +L       +GN++   G    +A  DR KG    + K+
Sbjct: 160 TSFVASDNVALGQTAAKWIADQLTKRYGSAKGNVVDLIGLVGTTAATDREKGFSDEIAKY 219

Query: 191 PGIHVLSDDQDGKGSREGGLNVMQLYLTRFPKIDAVFTINDPQAVGADLAARQLNR---- 246
           P I V++  Q+G   +E  LN M   L ++P+IDAVF  ND   VGA+ A     R    
Sbjct: 220 PDIKVVAR-QEGAFDQEKSLNAMTNILQKYPQIDAVFGANDDNTVGAEKAIDNAGRYKPL 278

Query: 247 ---GGILIASVDGAPDIEAALKANTLVQASASQDPWAIARTAVE-IGVGLMHGQAPANRT 302
                IL+   DG     +A++A     A+ SQ+P  +A  +++ +       + PAN  
Sbjct: 279 GDKQHILVIGADGTAQALSAIRAGK-QDATISQNPIQMAAKSLQFVADYSAKKEVPAN-- 335

Query: 303 VLLPPTLVTRANVN 316
              P  L+ ++N++
Sbjct: 336 YAWPTLLIDKSNID 349


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: 232
Number of extensions: 6
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 325
Length of database: 365
Length adjustment: 29
Effective length of query: 296
Effective length of database: 336
Effective search space:    99456
Effective search space used:    99456
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: 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