GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02871 in Paraburkholderia bryophila 376MFSha3.1

Align N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized)
to candidate H281DRAFT_02632 H281DRAFT_02632 carbohydrate ABC transporter membrane protein 2, CUT1 family

Query= reanno::Phaeo:GFF2752
         (280 letters)



>FitnessBrowser__Burk376:H281DRAFT_02632
          Length = 283

 Score =  159 bits (401), Expect = 8e-44
 Identities = 83/272 (30%), Positives = 144/272 (52%)

Query: 9   PFNSILAHGALITYTLIALFPVFVILVNSFKTRKAIFRDPLGLPTSDTFSLVGYQTVLKQ 68
           P++  L   +L     + L P+  +L+ S ++   + +            +  Y   L Q
Sbjct: 11  PWSRTLYKASLPVALFVWLLPMLAVLITSIRSSDELSQGDYWAWPKHFALIDNYGAALTQ 70

Query: 69  GDFFLYFQNSMIVTVVSLALVLLFGAMAAFALAEYRFKGNMLLGLYLALGIMIPIRIGTV 128
                YF NSM++TV S+   +L  +MA FALA YRF+GN+++      G  +P++I  +
Sbjct: 71  TPMLHYFANSMLITVPSVLGAILLASMAGFALATYRFRGNIVVLFTFVAGNFVPVQILMI 130

Query: 129 AILELMVDTGLVNTLTALILVYTAQGLPLAVFILSEFMKQVSDDLKNAGRIDGLSEYTIF 188
            + ++ +  GL NT+ ALI+ + A         L  F+KQ+  +L  A R++G SE+TI+
Sbjct: 131 PVRDMALKVGLFNTVWALIIFHVAFQTGFCTLFLRNFIKQLPFELIEAARVEGASEWTIY 190

Query: 189 FRLVLPLVRPAMATVAVFNMIPIWNDLWFPLILAPAEETKTLTLGSQVFIGQFVTDWNAV 248
            R+VLPL+RPA+A + +     +WND ++ L L   ++   +T+G     GQ+ T WN V
Sbjct: 191 ARIVLPLIRPALAALGILVFTFVWNDYFWALCLTQGDDAAPITVGVAALKGQWTTAWNLV 250

Query: 249 LSALSMAILPVMVLYVIFSRQLIRGITSGAVK 280
            +   +A LP ++++    +  + G+T GA K
Sbjct: 251 AAGSVLAALPSVLMFFAMQKHFVAGLTFGASK 282


Lambda     K      H
   0.330    0.143    0.414 

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: 230
Number of extensions: 14
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: 280
Length of database: 283
Length adjustment: 26
Effective length of query: 254
Effective length of database: 257
Effective search space:    65278
Effective search space used:    65278
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 47 (22.7 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