GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Phaeobacter inhibens BS107

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF1915 PGA1_c19470 ABC transporter, ATP-binding protein

Query= uniprot:A0A165KQ08
         (355 letters)



>FitnessBrowser__Phaeo:GFF1915
          Length = 363

 Score =  340 bits (872), Expect = 3e-98
 Identities = 181/359 (50%), Positives = 234/359 (65%), Gaps = 10/359 (2%)

Query: 1   MASSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEP 60
           M S +    ++ RFG    +VEVL+ +++ +  GEFL+L+G SGCGKSTLLN IAGL E 
Sbjct: 9   MTSHVSARDLSVRFG----AVEVLKSLNLDIQKGEFLVLLGASGCGKSTLLNTIAGLQEA 64

Query: 61  TEGEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRID 120
           TEG+I I  +NV    P+DR +AMVFQSYALYP ++V  N+ F L M K+PK E  K +D
Sbjct: 65  TEGQIWINDENVTWREPKDRGLAMVFQSYALYPKMTVRGNLAFGLRMNKVPKAEADKLVD 124

Query: 121 EVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAE 180
           E A +LQ+  LLDRRP +LSGGQRQRVA+GRAL R+  +FLFDEPLSNLDAKLR E+R E
Sbjct: 125 EAARVLQLEELLDRRPGELSGGQRQRVAIGRALVRKVDVFLFDEPLSNLDAKLRAELRVE 184

Query: 181 IKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIG 240
           +KRLHQ  G T +YVTHDQVEA+TL  RIAVMK GVVQQL +P+EIY RPAN YVA F+G
Sbjct: 185 LKRLHQELGATMIYVTHDQVEALTLADRIAVMKDGVVQQLDSPEEIYRRPANRYVAQFVG 244

Query: 241 SPTMNLLRGAVTGG------QFGIQGAALNLAPPPSSANEVLLGVRPEHLVMQETAPWRG 294
            P+MN + G VT         F +     NLA  P+   EV +G+RPEH+       +  
Sbjct: 245 LPSMNFVNGVVTESGAIQTEDFELALDQCNLASTPAPGTEVEIGIRPEHVHPANAGGFML 304

Query: 295 RVSVVEPTGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSEERL 353
            V +VE  G +  +       S+ +R D  T ++ G+ V + L P     F A++  R+
Sbjct: 305 DVGMVELLGSERLIWGKVGNTSIVMRDDPDTTIRSGDQVRINLKPGAFSVFSAKTGLRI 363


Lambda     K      H
   0.318    0.135    0.388 

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: 355
Number of extensions: 12
Number of successful extensions: 2
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: 355
Length of database: 363
Length adjustment: 29
Effective length of query: 326
Effective length of database: 334
Effective search space:   108884
Effective search space used:   108884
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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:

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