GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Phyllobacterium brassicacearum STM 196

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate WP_106712549.1 CU102_RS18395 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_003010955.1:WP_106712549.1
          Length = 354

 Score =  332 bits (852), Expect = 7e-96
 Identities = 182/379 (48%), Positives = 247/379 (65%), Gaps = 29/379 (7%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M +++  N+ K +    H  ++  +++I D EF++ VGPSGCGKST LRM+AGLE+I+ G
Sbjct: 1   MASVEFANVRKSF--GTHPVIKGVDIEIADGEFVILVGPSGCGKSTLLRMLAGLENISAG 58

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
            + I  +++N  +PK+RDIAMVFQNYALYPHM+V +NMAF L L+   K +I KRV  AA
Sbjct: 59  EIRIGGQVVNGLAPKERDIAMVFQNYALYPHMTVADNMAFSLTLKGAAKSEIEKRVKPAA 118

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
           EILGL+  L+R P  LSGGQRQRVAMGRAIVRD +VFL DEPLSNLDAKLRVAMRAEI +
Sbjct: 119 EILGLSHLLDRFPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVAMRAEIKE 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           +H+R+  TT+YVTHDQ EAMT+AD+IV+M            G +EQIG P ELY++PAN 
Sbjct: 179 LHQRLKTTTVYVTHDQIEAMTMADKIVVMHD----------GLVEQIGAPLELYDQPANL 228

Query: 241 FVAGFIGSPAMNFFEVTV---EKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRP 297
           FVA FIGSPAMN  +  +   + ++ V + G+ L + +  +         G  +  G+RP
Sbjct: 229 FVASFIGSPAMNMIKGRLDPNDTQKFVTEKGIVLPVAKAPDSA------KGLTLIYGLRP 282

Query: 298 EDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQ 357
           E        H T     + A+++V E  GSE+ + ++ G  + T   + R S  PGE V 
Sbjct: 283 E--------HMTIAQGGIPAEVVVIEPTGSETQMIMRVGGDDITGVFHQRISARPGEIVG 334

Query: 358 LTFNIAKGHFFDLETEKRI 376
           L+ +    + FD ET KR+
Sbjct: 335 LSIHAEATYLFDAETGKRL 353


Lambda     K      H
   0.318    0.135    0.379 

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: 385
Number of extensions: 15
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: 377
Length of database: 354
Length adjustment: 30
Effective length of query: 347
Effective length of database: 324
Effective search space:   112428
Effective search space used:   112428
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