GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Marinobacter adhaerens HP15

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter

Query= reanno::Smeli:SMc04256
         (361 letters)



>FitnessBrowser__Marino:GFF3011
          Length = 372

 Score =  329 bits (844), Expect = 6e-95
 Identities = 174/369 (47%), Positives = 244/369 (66%), Gaps = 8/369 (2%)

Query: 1   MTSVSVRDLSLNFGAVT--VLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDG 58
           M+ + +R +   +  V    L  +++DI  GEFL+L+G SGCGKSTL+N IAGL  ++DG
Sbjct: 1   MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60

Query: 59  QIFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRAS 118
            I +  ++++  EPKDR I MVFQSYALYP M+V +N++FGLK+  +P  EI++ V+R +
Sbjct: 61  SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120

Query: 119 EILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKR 178
           ++LQI PL+ +KP+ LSGGQ+QRVA+GRAL R   ++LFDEPLSNLDAKLR E+R EIK+
Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180

Query: 179 LHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPS 238
           LHQ LK T++YVTHDQIEA+TLADRIAV+K G +QQL  P  +Y+ PENLFVAGF+GSP+
Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240

Query: 239 MNFFRGEVEPKDG--RSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDG 296
           M+F    VE  +G  ++ VR           P     + G+KV+LG+RPEH+   + +  
Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVGKKVILGIRPEHITQPQDQKN 300

Query: 297 EPTHQA----VVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASI 352
           + T  A     +++ EP G D +  +     ++  RI  +     G T  L FDM     
Sbjct: 301 DQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAELMFDMKKVVF 360

Query: 353 FDAESENRL 361
           FD E+E R+
Sbjct: 361 FDPETEKRI 369


Lambda     K      H
   0.320    0.137    0.392 

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: 447
Number of extensions: 18
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: 361
Length of database: 372
Length adjustment: 30
Effective length of query: 331
Effective length of database: 342
Effective search space:   113202
Effective search space used:   113202
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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:

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