GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0029 in Paraburkholderia bryophila 376MFSha3.1

Align TM0029, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate H281DRAFT_06102 H281DRAFT_06102 peptide/nickel transport system permease protein

Query= TCDB::Q9WXN6
         (280 letters)



>FitnessBrowser__Burk376:H281DRAFT_06102
          Length = 304

 Score =  132 bits (332), Expect = 9e-36
 Identities = 80/270 (29%), Positives = 146/270 (54%), Gaps = 11/270 (4%)

Query: 12  NKKFIIGFSIFLFFLFLGIFGPMFYRVDPT-EMTWDYEQPPSS-AHPLGTDTYGRDVLAQ 69
           N   + GF+I +  + + I GP     DP  ++  D   PP S +H LGTD  GRD+L++
Sbjct: 38  NPLSVFGFAILMVLVIVAIIGPWIAPHDPLRQVLSDRLLPPGSPSHWLGTDQLGRDILSR 97

Query: 70  LLHGIRSSLYIGFLAAIISLVIGTIIGSFSAVKRGIVDDVLMGITNIVLTTPSILIAILI 129
           +++G R +L I  L  ++ + IG +IG+ +    G VD+VLM +T+I L  P I++A+  
Sbjct: 98  IIYGSRLTLSIAILVVVVVVPIGLMIGTTAGFFGGWVDNVLMRVTDIALAFPKIVLALAF 157

Query: 130 ASYLKVRSVEMVAVILGLFQWPWFARAIRAQLMSVMSREYVYLSVMAGYSDLRLVIEDLI 189
           A+ L    +  V + + +  WP +AR  RA+ + ++  +++ ++ + G S+LR+++  ++
Sbjct: 158 AAALGPGVINAV-IAISITAWPAYARLARAETLRLVQADFIQVARLQGASNLRILLRYVV 216

Query: 190 PTIATYAFMSFVLFINGGIMGEAGLSLIGLGPTQGISLGIMLQWAVLMEAVRRGL---WW 246
           P   +   +   L + G I+  AGL  +GLG           +W  ++ + R  L   WW
Sbjct: 217 PLCMSSVIVRATLDMAGIILTVAGLGFLGLGAQPPSP-----EWGFMVASGRNVLLDSWW 271

Query: 247 WFVPPGLAIVAVTASLLVISTAMDEVFNPR 276
               PG AI+ V+ +  ++   + +VF+PR
Sbjct: 272 VATIPGFAILLVSLAFNLLGDGLRDVFDPR 301


Lambda     K      H
   0.330    0.144    0.441 

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: 196
Number of extensions: 16
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: 280
Length of database: 304
Length adjustment: 26
Effective length of query: 254
Effective length of database: 278
Effective search space:    70612
Effective search space used:    70612
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: 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