GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05255 in Pantoea rwandensis LMG 26275

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_084931761.1 HA51_RS02830 hypothetical protein

Query= uniprot:D8J112
         (347 letters)



>NCBI__GCF_002095475.1:WP_084931761.1
          Length = 323

 Score =  233 bits (593), Expect = 7e-66
 Identities = 127/303 (41%), Positives = 191/303 (63%), Gaps = 9/303 (2%)

Query: 43  LLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAV 102
           LL++++ FSF SP F  V NL++ILQ +++N ++A+  T VII+ GIDLSVG      AV
Sbjct: 30  LLIIVVTFSFLSPVFFTVPNLLNILQQSSINALIALGMTLVIISGGIDLSVGPTAALSAV 89

Query: 103 MAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVI 162
           + G  L   G+P+P+ I A +  GAL G  SGM++A   + PFI TLG + L + ++L+ 
Sbjct: 90  L-GATLMVAGVPVPVAILATLGIGALCGVFSGMLVAYAGLQPFIVTLGGLSLFRAIALIY 148

Query: 163 SGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTF 222
           +G  P++    E F +I    + G       IP  ++I+ ++A+   +++NKT  G Y  
Sbjct: 149 TGGNPVFGIPME-FRSIINSDVFG-------IPTPIIIVAVIALVLWLVMNKTPLGEYIL 200

Query: 223 ALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAA 282
           A+G NEEA R++GV V   KV V+  SG +  +A LI+  RL +A+P +G  +ELDAIAA
Sbjct: 201 AVGGNEEAARVAGVPVKRTKVTVFIISGTLASLASLILIGRLGAAEPTIGNLWELDAIAA 260

Query: 283 VVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILR 342
             IGG SL GG G+I+GTIIGA I+  L NGL ++++   +Q + TG+III+A+ +D   
Sbjct: 261 AAIGGASLMGGKGSIVGTIIGAIILGALRNGLTLLNIQAFYQLLATGLIIIIAMLIDRAT 320

Query: 343 RRR 345
           R R
Sbjct: 321 RGR 323


Lambda     K      H
   0.326    0.139    0.398 

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: 242
Number of extensions: 14
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: 347
Length of database: 323
Length adjustment: 28
Effective length of query: 319
Effective length of database: 295
Effective search space:    94105
Effective search space used:    94105
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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