GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Marivita geojedonensis DPG-138

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_085637757.1 MGEO_RS11955 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::pseudo5_N2C3_1:AO356_00010
         (365 letters)



>NCBI__GCF_002115805.1:WP_085637757.1
          Length = 365

 Score =  313 bits (803), Expect = 4e-90
 Identities = 169/363 (46%), Positives = 242/363 (66%), Gaps = 10/363 (2%)

Query: 4   LKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTIELD 63
           L I+NL K +    I+K I++ ++  +F+V VGPSGCGKSTLL  IAGLE +T G+I + 
Sbjct: 5   LDIKNLYKSYGTTEILKDINVSIEPGDFLVLVGPSGCGKSTLLNCIAGLEPITGGSINIG 64

Query: 64  GRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARILEL 123
           G+D+T V+P  RD+AMVFQ+YALYP MTV KN++F + + G  +   +RK+A+ A+ L++
Sbjct: 65  GKDMTHVSPKDRDIAMVFQSYALYPTMTVAKNITFGMKVRGVDQATQDRKLAQVAQQLQI 124

Query: 124 GSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLHKEL 183
             LL+R+P QLSGGQRQRVA+GRA+VR+PK+FLFDEPLSNLDA LRV+ R E+  LH  L
Sbjct: 125 EPLLNRRPGQLSGGQRQRVAMGRALVRDPKLFLFDEPLSNLDAKLRVEMRTEIKSLHHNL 184

Query: 184 QATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKMGFLQ 243
            A+M+YVTHDQ+EAMTLATK+VV+  G I+QIGSP E+Y+ PANLFVA F+G+P M  + 
Sbjct: 185 GASMVYVTHDQIEAMTLATKIVVMKGGVIQQIGSPAEIYNRPANLFVADFMGSPAMNLIP 244

Query: 244 ATVH-AVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPEHLT----LGAEGQVLV 298
           A  H A   + +E+   SG  +++  D+    + + V +G+RPE +      GAE     
Sbjct: 245 AKAHRADEGTRIEITRKSGEPIVL-TDTKNRDLPEDVILGVRPEDIADPDLRGAEAAQAA 303

Query: 299 --TTDVTERLGSDTFCHVNVDSGESLTVRVQGDCEVPYAARRYLTLDVAHCHLF-DESGL 355
               D+ E  G+DTF  + +  G+ +T R+  +        + L+ D+     F  E+GL
Sbjct: 304 ECLIDMVEPAGADTFAVMQL-GGKHVTARLHAETTAKPGQPKRLSFDLGKVSYFAPETGL 362

Query: 356 SVS 358
            ++
Sbjct: 363 RLN 365


Lambda     K      H
   0.319    0.136    0.381 

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: 358
Number of extensions: 16
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: 365
Length of database: 365
Length adjustment: 30
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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