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_106711245.1 CU102_RS11585 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_003010955.1:WP_106711245.1
          Length = 355

 Score =  336 bits (861), Expect = 7e-97
 Identities = 187/376 (49%), Positives = 235/376 (62%), Gaps = 28/376 (7%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M ++ + ++ K Y N     +   ++DI D EF++ VGPSGCGKST LRMIAGLE+IT G
Sbjct: 1   MASVSIRDVTKTYGNVN--VMHGVSVDIEDGEFVILVGPSGCGKSTLLRMIAGLEEITGG 58

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
            + I  +++ND   K+RDIAMVFQNYALYPHM+V +NM F L L+   K +   RV  AA
Sbjct: 59  EIAIGSRVVNDLPAKERDIAMVFQNYALYPHMTVADNMGFALMLKNAPKQEKESRVGRAA 118

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
           EILGL + L+R P  LSGGQRQRVAMGRAIVRD +VFL DEPLSNLDAKLRV MR+EI  
Sbjct: 119 EILGLEKLLDRFPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRSEIKG 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           +H+R+G T +YVTHDQ EAMT+AD+IV+M            G +EQIGTP +LY+ PAN 
Sbjct: 179 LHQRLGTTIVYVTHDQIEAMTMADKIVVMKD----------GLVEQIGTPLDLYDYPANL 228

Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDI 300
           FVAGFIGSPAMNF +  VE    V  DG+ L LP G     E         T GIRPE  
Sbjct: 229 FVAGFIGSPAMNFIKGKVENGAFVTPDGVKLPLPSGLGSTAE--------ATYGIRPE-- 278

Query: 301 SSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQLTF 360
                 H     + +   + V E  GSE M+  K G+ E +     R S  PG+ + +  
Sbjct: 279 ------HIRMAESGIPVKVDVVEPTGSEIMVVGKIGAQEISCLFRDRLSIKPGDTIHVAI 332

Query: 361 NIAKGHFFDLETEKRI 376
           + A  H FD+ +  RI
Sbjct: 333 DPATSHLFDMASGARI 348


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: 389
Number of extensions: 16
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: 355
Length adjustment: 30
Effective length of query: 347
Effective length of database: 325
Effective search space:   112775
Effective search space used:   112775
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