GapMind for catabolism of small carbon sources

 

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

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_085637757.1 MGEO_RS11955 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= uniprot:Q6MNM2
         (347 letters)



>NCBI__GCF_002115805.1:WP_085637757.1
          Length = 365

 Score =  299 bits (766), Expect = 7e-86
 Identities = 166/359 (46%), Positives = 228/359 (63%), Gaps = 20/359 (5%)

Query: 4   IQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISID 63
           +   N+ KS+G+ ++LK I++ I PG+FLVLVGPSGCGKSTLL  +AGLE    G+I+I 
Sbjct: 5   LDIKNLYKSYGTTEILKDINVSIEPGDFLVLVGPSGCGKSTLLNCIAGLEPITGGSINIG 64

Query: 64  GKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQI 123
           GK +  + P++RDIAMVFQSYALYP MTVA+N+ FG+K++ +  A   +++ ++++ LQI
Sbjct: 65  GKDMTHVSPKDRDIAMVFQSYALYPTMTVAKNITFGMKVRGVDQATQDRKLAQVAQQLQI 124

Query: 124 KHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNS 183
           + LL+R+P +LSGGQRQRVA+GRAL R   + LFDEPLSNLDA LR +MR EIK LHHN 
Sbjct: 125 EPLLNRRPGQLSGGQRQRVAMGRALVRDPKLFLFDEPLSNLDAKLRVEMRTEIKSLHHNL 184

Query: 184 KSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFL- 242
            ++M+YVTHDQ+EA TL  +I V+K GVI+QIG+P+EIY+RP N F+A F+GSP MN + 
Sbjct: 185 GASMVYVTHDQIEAMTLATKIVVMKGGVIQQIGSPAEIYNRPANLFVADFMGSPAMNLIP 244

Query: 243 -------EGAVL-------EKIPWPEARK----ADQILGIRPDAFALNQGPLGTQEVALG 284
                  EG  +       E I   + +      D ILG+RP+  A +    G +     
Sbjct: 245 AKAHRADEGTRIEITRKSGEPIVLTDTKNRDLPEDVILGVRPEDIA-DPDLRGAEAAQAA 303

Query: 285 DFQIDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFDKKTGL 343
           +  ID+ E  G        L G +V   + +       Q   L  DL K   F  +TGL
Sbjct: 304 ECLIDMVEPAGADTFAVMQLGGKHVTARLHAETTAKPGQPKRLSFDLGKVSYFAPETGL 362


Lambda     K      H
   0.318    0.136    0.383 

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: 335
Number of extensions: 12
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: 347
Length of database: 365
Length adjustment: 29
Effective length of query: 318
Effective length of database: 336
Effective search space:   106848
Effective search space used:   106848
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 24 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