GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Streptococcus massiliensis 4401825

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_018371126.1 BN415_RS08120 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::BFirm:BPHYT_RS16095
         (369 letters)



>NCBI__GCF_000341525.1:WP_018371126.1
          Length = 377

 Score =  332 bits (850), Expect = 1e-95
 Identities = 192/376 (51%), Positives = 235/376 (62%), Gaps = 30/376 (7%)

Query: 1   MASVTLRNIRKAYDENE--VMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGG 58
           M  V L  + K Y  +E   + D NLDI D EF+VFVGPSGCGKST +RMIAGLEDI+ G
Sbjct: 1   MVQVKLDKVYKRYPNSEHYSVEDFNLDIQDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60

Query: 59  DLTIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAA 118
           +  IDG  +NDVAP  R IAMVFQ+YALYPHMT+Y+NMAFGLKL    K EID  VR AA
Sbjct: 61  EFLIDGQVMNDVAPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYAKDEIDRRVREAA 120

Query: 119 KILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFAR 178
           +IL +   LDRKP  LSGGQRQRVA+GRAI R  K+FL DEPLSNLDA LRV MR E A+
Sbjct: 121 EILGLIEFLDRKPADLSGGQRQRVAMGRAIVRDSKIFLMDEPLSNLDAKLRVSMRAEIAK 180

Query: 179 LHDELKTTMIYVTHDQVEAMTLADKIVVLSA----------GNLEQVGSPTMLYHAPANR 228
           LH  +  T IYVTHDQ EAMTLAD+IV++SA          G +EQ+GSP  LY+ PAN+
Sbjct: 181 LHRRIGATTIYVTHDQTEAMTLADRIVIMSATKNPSGTGTIGRIEQIGSPQELYNTPANK 240

Query: 229 FVAGFIGSPKMNFM-----EGVVQSVTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGI 283
           FVAGFIGSP MNF      +GV+ S    G+++R   G  +R  +E      G ++  GI
Sbjct: 241 FVAGFIGSPAMNFFKVALKDGVISS--EQGLSLRLPEG--KRKLLEDKGY-NGKELIFGI 295

Query: 284 RPEHLHVGM------AEDGISARTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHTKG 337
           RPE +           E  ++A  +  E LG  + LY  S +     ++R+   + H  G
Sbjct: 296 RPEDIKASQLELDAYPESVVTAEVIVSELLGSESMLY--SKLGDTEFVSRVEARDLHNPG 353

Query: 338 ETQKLGATPEHCHLFD 353
           E  KL       H FD
Sbjct: 354 EHVKLAFNVNKGHFFD 369


Lambda     K      H
   0.320    0.135    0.384 

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: 377
Number of extensions: 19
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: 369
Length of database: 377
Length adjustment: 30
Effective length of query: 339
Effective length of database: 347
Effective search space:   117633
Effective search space used:   117633
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: 50 (23.9 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