GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02871 in Herbaspirillum seropedicae SmR1

Align N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized)
to candidate HSERO_RS22745 HSERO_RS22745 sugar ABC transporter permease

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



>FitnessBrowser__HerbieS:HSERO_RS22745
          Length = 300

 Score =  353 bits (907), Expect = e-102
 Identities = 172/265 (64%), Positives = 217/265 (81%)

Query: 16  HGALITYTLIALFPVFVILVNSFKTRKAIFRDPLGLPTSDTFSLVGYQTVLKQGDFFLYF 75
           H  L  Y +IALFP+ +IL+NS KTR AIF  P+ LPT++T +  G+Q VL    F LYF
Sbjct: 36  HTVLCLYAVIALFPIALILINSVKTRNAIFEGPMALPTAETLTFAGFQKVLAGTHFLLYF 95

Query: 76  QNSMIVTVVSLALVLLFGAMAAFALAEYRFKGNMLLGLYLALGIMIPIRIGTVAILELMV 135
            NS+ VTV +L L++LFGAMAA+AL EYRF GN  L  ++A+GIMIPIR+GTV+IL+L+V
Sbjct: 96  GNSLAVTVAALFLIVLFGAMAAWALTEYRFFGNRALNFFIAIGIMIPIRLGTVSILQLVV 155

Query: 136 DTGLVNTLTALILVYTAQGLPLAVFILSEFMKQVSDDLKNAGRIDGLSEYTIFFRLVLPL 195
              L+NT TAL+LVYTAQGLPLAV ILSEFM+Q+  +LK+A R DG+ E +IFFR++LPL
Sbjct: 156 ALDLINTRTALVLVYTAQGLPLAVMILSEFMRQIPGELKDAARCDGVGELSIFFRVILPL 215

Query: 196 VRPAMATVAVFNMIPIWNDLWFPLILAPAEETKTLTLGSQVFIGQFVTDWNAVLSALSMA 255
           +RPA+ATVAVF MIP WNDLWFPLILAP E+T+T+TLG Q FIGQ+ TDWN+VL+ALSMA
Sbjct: 216 LRPAIATVAVFTMIPAWNDLWFPLILAPGEDTRTVTLGVQQFIGQYATDWNSVLAALSMA 275

Query: 256 ILPVMVLYVIFSRQLIRGITSGAVK 280
           ++PV++LY+ FSRQLIRG+TSGAVK
Sbjct: 276 VIPVLLLYMAFSRQLIRGLTSGAVK 300


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: 311
Number of extensions: 6
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: 300
Length adjustment: 26
Effective length of query: 254
Effective length of database: 274
Effective search space:    69596
Effective search space used:    69596
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