GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS05255 in Phaeobacter inhibens BS107

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC

Query= uniprot:D8J112
         (347 letters)



>lcl|FitnessBrowser__Phaeo:GFF2276 PGA1_c23080 ribose transport
           system permease protein RbsC
          Length = 324

 Score =  191 bits (486), Expect = 2e-53
 Identities = 120/312 (38%), Positives = 180/312 (57%), Gaps = 18/312 (5%)

Query: 37  LLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTM 96
           L+AFA   L I+ F+ A+P F+ +DN  ++++S+A+ GV+A+  T+V+I+  +DLSVG+M
Sbjct: 19  LIAFA---LFIIGFTIANPKFLTLDNFENVVRSSAILGVMALGVTFVVISGNLDLSVGSM 75

Query: 97  MTFCAVMAGVVLTNWG--MPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMML 154
           M+F  ++   +    G  + +P   A  +  GAL G++ G     LK+   I TLGM+  
Sbjct: 76  MSFSTIVVLDLHDKLGPTLAIPAMFAMTLCLGALIGFLVGY----LKLNSLIVTLGMLSA 131

Query: 155 LKGLSLVISGTRPIYFNDTEG--FSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIIL 212
           + GL+L  SG + +   D EG  F+   Q +++G       I   +LI   +A    IIL
Sbjct: 132 IHGLTLTYSGGKNMDIADKEGTWFAIFGQGNILG-------IQTPILIFIALAALLGIIL 184

Query: 213 NKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALG 272
            KT FGR  +A+G N  A   SG++        Y  S      AGLI ASR   +Q  +G
Sbjct: 185 AKTPFGRKVYAVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMGSQNTVG 244

Query: 273 QGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVII 332
           QG EL+ +AAV++GG SL GG+GTI  T+IG  I+  + NGL ++ +    Q VVT +II
Sbjct: 245 QGLELEVLAAVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYVVTWIII 304

Query: 333 ILAVYLDILRRR 344
           ILAV+LDI  +R
Sbjct: 305 ILAVWLDIAAKR 316


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: 221
Number of extensions: 12
Number of successful extensions: 4
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: 324
Length adjustment: 28
Effective length of query: 319
Effective length of database: 296
Effective search space:    94424
Effective search space used:    94424
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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